from Tkinter import * import Pmw import pymol from pymol import cmd import tkColorChooser import re import string from pymol import cmd from Tkinter import * import tkSimpleDialog import tkMessageBox import string import os from tkFileDialog import askopenfilename, asksaveasfilename import re import urllib2 import StringIO import gzip import time import types import os from pymol import util import pickle import random import linecache import Pmw import urllib from pymol import selector from pymol import cmd from pymol import _cmd from cmd import* try: PYMOL_PATH=os.environ['PYMOL_PATH'] except KeyError: PYMOL_PATH='./' Pmw.initialise() #--------------------------------------------------------------- # Link our GUI to PyMOL #--------------------------------------------------------------- def __init__(self): self.menuBar.addmenuitem('Plugin', 'command', 'Easy GUI', label = 'ProMOL 3.02', command = lambda s=self : PGUI(s)) #-----------------------Version 1-------------------------------# #--------------------------------------------------------------------# # # # PDBParser # # # # # # # # Parse PDB files and pull out the useful information # # # #---------------------------------------------------------------# class PDBParser: #Most of this not called anymore, not enough time to sift through #and delete though global true #------Constructor---------- def __init__(self): #self.filename=filename self.author = '' self.true=1 self.title = '' self.ref = '' self.journal = '' self.name='' self.hetero='' self.hlist=[] self.chains={} self.classify='' self.idList=[] self.allHet=[] self.helices=[] # Read in the PDB file line by line # Call method depending on what line starts with def readFile(self, file): in_file = open(file, 'r') j=re.compile("^JRNL") h=re.compile("^HEADER") t=re.compile("^TITLE") c=re.compile("^COMPND") ht=re.compile("^HET ") s=re.compile("^SEQRES") hel=re.compile("^HELIX") while self.true: line=in_file.readline() if line == "": break line = line[:-1] #Molecular Classification if h.match(line): self.classify=string.strip(line[10:50]) #Molecule Name elif t.match(line): temp=string.strip(line[10:70]) self.name=self.name+' '+temp elif c.match(line) and self.name=='': temp=string.strip(line[10:70]) self.name=self.name+' '+temp #Journal Entry elif j.match(line): self.getJrnl(line) #Hetero Atoms elif ht.match(line): self.getHet(line) elif s.match(line): self.getSeq(line) # find out if regular expression was found elif hel.match(line): #print 'HELIX FOUND: ' + line self.get_helix_entry(line) self.hetero=string.join(self.hlist, sep=', ') self.journal=self.author+"\n"+self.title+"\n"+self.ref in_file.close() # Get journal entry information def getJrnl(self, line): temp2=[] a=re.compile("AUTH") t=re.compile("TITL") r=re.compile("REF") if a.match(line[12:18]): self.author = self.author+string.strip(line[19:70]) if t.match(line[12:18]): self.title = self.title+" "+string.strip(line[19:70]) if r.match(line[12:18]): st = string.strip(line[19:70]) temp=string.split(st) temp2.append(temp) for list in temp2: for item in list: self.ref = self.ref+' '+item #Get list of hetero atoms found in molecule def getHet(self, line): temp = string.strip(line[7:10]) id = string.strip(line[13:17]) if self.hlist.count(temp)==0: self.hlist.append(temp) #self.idList.append(id) else: pass chain=string.strip(line[11:13]) if chain == "": id = 'resi '+ id else: id = chain+"/"+id+"/" self.idList.append(id) #Get sequence/chain information def getSeq(self, line): chainID = line[11] seq = string.strip(line[19:70]) if self.chains.has_key(chainID): temp =self.chains[chainID] seq =temp+' '+seq self.chains[chainID]=seq else: self.chains[chainID]=seq # Get Helix start/stop locations # (adds a helix object to an array) def get_helix_entry(self, line): start = string.strip(line[21:25]) end = string.strip(line[33:37]) chain = string.strip(line[19:20]) tempHelix = Helix(start,end,chain) self.helices.append(tempHelix) #------------------------------------------------------------------# # # # Helix Class # # # # # # # # Helix Objects (used in movies) # # # #------------------------------------------------------------------# class Helix: def __init__(self, start, end, chain): self.start = start self.end = end self.chain = chain def getStart(self): return self.start def getEnd(self): return self.end def getChain(self): return self.chain #---------------------------------------------------------------# # # # Chime Converter # # # # # # # # Handle the entry of Chime commands # # # #---------------------------------------------------------------# class ChimeConverter: #------Constructor---------- def __init__(self): # initialize variables self.cmdLine = ' ' self.command = ' ' self.results = ' ' self.args = [] self.argsLength = 0 self.rpsts = {'cartoon':'cartoon', 'cartoons':'cartoon', 'backbone':'ribbon', 'spacefill':'spheres', 'dots':'dots', 'wireframe':'lines', 'ribbons':'cartoon', 'ribbon':'cartoon'} self.coloring={'colour':'color', 'color':'color', 'background':'bg_color'} self.individuals={'center':'zoom', 'centre':'zoom'} self.selections={'dna':'resn a+g+c+t+u', 'protein':'resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR+ACD+ACE+ALB+ALI+ABU+ARO+ASX+BAS+BET+FOR+GLX+HET+HSE+HYP+HYL+ORN+PCA+SAR+TAU+TER+THY+UNK+MSE', 'hydrophobic':'resn ALA+ILE+LEU+MET+PHE+PRO+TRP+VAL', 'hydrophilic':'resn THR+SER+ARG+ASN+ASP+GLN+GLU+HIS+LYS', 'acidic':'resn ASP+GLU', 'basic':'resn ARG+HIS+LYS'} # parse the command def parseIt(self, input, commLine, resultBox): self.cmdLine = commLine self.results = resultBox # get rid of capitalizations and leading/ending # white space ui = input.lower() ui = ui.strip() # store the command self.args = ui.split() self.argsLength = len(self.args) self.command = self.args[0] # representations if self.command in self.rpsts.keys(): # repeat the command back to the user self.results.appendtext('Chime: ' + ui + '\n') self.on_off_conversions() # coloring stuff elif self.command in self.coloring.keys(): # repeat the command back to the user self.results.appendtext('Chime: ' + ui + '\n') self.coloring_conversions() # commands without additional arguments elif self.command in self.individuals.keys(): # repeat the command back to the user self.results.appendtext('Chime: ' + ui + '\n') self.convert_individual() # action commands ( such as spin ) elif self.command == 'spin': self.results.appendtext('Chime: ' + ui + '\n') self.convert_spin() # selections from the user elif self.command == 'select': self.results.appendtext('Chime: ' + ui + '\n') self.convert_selections() # if the command is not recognized, let the user know else: self.results.appendtext('Error: Chime command not recognized.\n\n') self.cmdLine.clear() #self.cmdLine.focus_force() #-----------------------------------------# # Chime Conversion Methods # #-----------------------------------------# # handle on/off type commands def on_off_conversions(self): pymShow = 'PyMOL: show '+ self.rpsts[self.command] + ', all\n\n' pymHide = 'PyMOL: hide ' + self.rpsts[self.command]+ ', all\n\n' if self.args[0] == 'backbone': cmd.hide('everything') cmd.show('ribbon','all') pymShow = 'PyMOL: hide everything; show '+ self.rpsts[self.command] + ', all\n\n' if self.argsLength > 1: switch = self.args[1] if switch == 'on': cmd.show(self.rpsts[self.command],'all') self.results.appendtext(pymShow) else: cmd.hide(self.rpsts[self.command],'all') self.results.appendtext(pymHide) else: cmd.show(self.rpsts[self.command],'all') self.results.appendtext(pymShow) # background command def coloring_conversions(self): selections = cmd.get_names('all') currentSel = selections[len(selections)-1] #print currentSel if self.argsLength > 1: pymCmd = 'PyMOL: '+self.coloring[self.command]+' '+self.args[1] if self.command=='color' or self.command=='colour': cmd.color(self.args[1],currentSel) pymCmd = pymCmd + ', '+currentSel+'\n\n' elif self.command=='background': cmd.bg_color(self.args[1]) pymCmd = pymCmd + '\n\n' self.results.appendtext(pymCmd) else: self.results.appendtext('Usage: '+self.command+' + [color]\n\n') def convert_spin(self): pymSpin = 'PyMOL: mset 1 x180; util.mroll(1,180,1); mplay\n\n' if self.argsLength > 1: if self.args[1] == 'off': cmd.do('mstop; mset') pymSpin = 'PyMOL: mstop; mset\n\n' else: cmd.do('mset 1 x180; util.mroll(1,180,1);mplay') else: cmd.do('mset 1 x180; util.mroll(1,180,1);mplay') self.results.appendtext(pymSpin) # convert chime selections def convert_selections(self): try: if self.argsLength > 1: pymSelect = 'PyMOL: select '+self.selections[self.args[1]]+'\n\n' self.results.appendtext(pymSelect) cmd.select(self.selections[self.args[1]]) else: self.results.appendtext('Usage: select [selection]') except: import tkMessageBox tkMessageBox.showinfo('Error', 'That is not a supported command') # 'individual command' conversions def convert_individual(self): pymShow = 'PyMOL: '+self.individuals[self.command]+'\n\n' cmd.do(self.individuals[self.command]) self.results.appendtext(pymShow) #---------------------------------------------------------------# # # # GUI Class # # # # # # # # The look of the interface # # # #---------------------------------------------------------------# class PGUI: global splash global TACOBUENO global GLYTACO global ASPTACO global PROTACO global METTACO global PHETACO global ASNTACO global ARGTACO global SERTACO global CYSTACO global THRTACO global GLUTACO global TRPTACO global GLNTACO global VALTACO global HISTACO global ILETACO global LEUTACO global LYSTACO global TYRTACO global ALAGUM global ARGGUM global ASNGUM global ASPGUM global CYSGUM global GLUGUM global GLNGUM global GLYGUM global HISGUM global ILEGUM global LEUGUM global LYSGUM global METGUM global PHEGUM global PROGUM global SERGUM global THRGUM global TRPGUM global TYRGUM global VALGUM class script: global script global AminoMenuList global AminoList global AlphaSequence global alphaSequence #-----Brett's and Charlie's amino acid images--------- #3D Reference Image TACOBUENO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/TACOBUENO.GIF") GLYTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLYTACO.GIF") ASPTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ASPTACO.GIF") PROTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/PROTACO.GIF") METTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/METTACO.GIF") PHETACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/PHETACO.GIF") ASNTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ASNTACO.GIF") ARGTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ARGTACO.GIF") SERTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/SERTACO.GIF") CYSTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/CYSTACO.GIF") THRTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/THRTACO.GIF") GLUTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLUTACO.GIF") TRPTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/TRPTACO.GIF") GLNTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLNTACO.GIF") VALTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/VALTACO.GIF") HISTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/HISTACO.GIF") ILETACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ILETACO.GIF") LEUTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/LEUTACO.GIF") LYSTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/LYSTACO.GIF") TYRTACO = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/TYRTACO.GIF") #2D Reference Image ALAGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ALAGUM.GIF") GLYGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLYGUM.GIF") ASPGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ASPGUM.GIF") PROGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/PROGUM.GIF") METGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/METGUM.GIF") PHEGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/PHEGUM.GIF") ASNGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ASNGUM.GIF") ARGGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ARGGUM.GIF") SERGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/SERGUM.GIF") CYSGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/CYSGUM.GIF") THRGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/THRGUM.GIF") GLUGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLUGUM.GIF") TRPGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/TRPGUM.GIF") GLNGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/GLNGUM.GIF") VALGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/VALGUM.GIF") HISGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/HISGUM.GIF") ILEGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/ILEGUM.GIF") LEUGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/LEUGUM.GIF") LYSGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/LYSGUM.GIF") TYRGUM = PhotoImage(file="./modules/pmg_tk/startup/AminoPics/TYRGUM.GIF") # Welcome tab image splash = PhotoImage(file="./modules/pmg_tk/startup/splashmol.GIF") #Amino Acid Abbre List for Menus AminoMenuList = ('','ala','arg','asn','asp','cys','gln','glu','gly','his','ile','leu','lys','met','phe','pro','ser','thr','trp','tyr','val') #Amino Acid Array for validation AminoList = ('ala','arg','asn','asp','cys','gln','glu','gly','his','ile','leu','lys','met','phe','pro','ser','thr','trp','tyr','val') #A - Z AlphaSequence = [ "%c" % (x) for x in range(ord('A'), ord('Z')+1)] #a - z alphaSequence = [ "%c" % (x) for x in range(ord('a'), ord('z')+1)] #--------------------------------------# # # # PRESETS METHODS # # # #--------------------------------------# #All initially Larua's and Chris's code, but modified by Brett and Charlie #none of the preset views worked when a PDB file was loaded #through Pymol, all had to be loaded through EZViz for parsing #reasons, so all presets were modified, and some completely redone #to allow for a user to load it from wherever they want, whenever they #want, and still have the view work. Only functionality loss was distinguishin between DNA and RNA #---------------------Version 2-------------------------# def write_script(self, tag): if tag == 'Off': self.script ='0' if tag=='On': #write a scritp try: self.script = '1' import tkFileDialog self.Q = tkFileDialog.asksaveasfilename(defaultextension=".py", initialdir="./modules/pmg_tk/startup/Scripts") cmd.do('log_open %s,a' %(self.Q)) self.f=open(self.Q, 'w') except: pass def set_defaults(self): cmd.hide('everything','all') cmd.set('transparency','0.0','all') cmd.set('cartoon_transparency','0.0','all') cmd.set('transparency','0','all') cmd.set('sphere_transparency','0.0','all') cmd.set('stick_transparency','0.0','all') cmd.set('sphere_scale','0.7','all') cmd.cartoon('automatic', 'all') cmd.set('stick_radius','0.2','all') if self.script == '1': self.f.write('''cmd.hide("everything","all") cmd.set("transparency","0.0","all") cmd.set("cartoon_transparency","0.0","all") cmd.set("transparency","0","all") cmd.set("sphere_transparency","0.0","all") cmd.set("stick_transparency","0.0","all") cmd.set("sphere_scale","0.7","all") cmd.cartoon("automatic", "all") cmd.set("stick_radius","0.2","all")\n''') self.delcrea() # emphasize DNA def show_dna_rna(self): import tkMessageBox points = 0 self.delcrea() self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() try: cmd.set('cartoon_ring_mode' ,'1') if self.script == '1': self.f.write('''cmd.set('cartoon_ring_mode' ,'1')\n''') if 'nucleic_acid' in objects: self.set_defaults() if 'protein' in objects: cmd.show('cartoon','protein') cmd.color('gray60','protein') if self.script == '1': self.f.write('''cmd.show('cartoon','protein') cmd.color('gray60','protein')\n''') if 'ligands' in objects: cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.4','ligands') cmd.set('sphere_scale','0.4','ligands') cmd.color('orange', 'ligands') if self.script == '1': self.f.write('''cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.4','ligands') cmd.set('sphere_scale','0.4','ligands') cmd.color('orange', 'ligands')\n''') if 'nucleic_acid' in objects: cmd.show('cartoon', 'nucleic_acid') cmd.color('lightblue','resn a') cmd.color('orange','resn c') cmd.color('salmon','resn g') cmd.color('palegreen','resn t') cmd.color('paleyellow', 'resn u') if self.script == '1': self.f.write('''cmd.show('cartoon', 'nucleic_acid') cmd.color('lightblue','resn a') cmd.color('orange','resn c') cmd.color('salmon','resn g') cmd.color('palegreen','resn t') cmd.color('paleyellow', 'resn u')\n''') points = points + 3 if points == 3: tkMessageBox.showinfo('Nucleic Acid Key','Adenine = light blue\nCytosine = orange\nGuanine = salmon red\nThymine = light green\nUracil = light yellow') else: tkMessageBox.showinfo("Error", "There is no DNA or RNA in this molecule.") except: if 'nucleic_acid' in objects: self.set_defaults() if 'protein' in objects: cmd.show('cartoon','protein') cmd.color('gray60','protein') if self.script == '1': self.f.write('''cmd.show('cartoon','protein') cmd.color('gray60','protein')\n''') if 'ligands' in objects: cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.4','ligands') cmd.set('sphere_scale','0.4','ligands') cmd.color('orange', 'ligands') if self.script == '1': self.f.write('''cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.4','ligands') cmd.set('sphere_scale','0.4','ligands') cmd.color('orange', 'ligands')\n''') if 'nucleic_acid' in objects: cmd.show('cartoon', 'nucleic_acid') cmd.color('lightblue','resn a') cmd.color('orange','resn c') cmd.color('salmon','resn g') cmd.color('palegreen','resn t') cmd.color('paleyellow', 'resn u') if self.script == '1': self.f.write('''cmd.show('cartoon', 'nucleic_acid') cmd.color('lightblue','resn a') cmd.color('orange','resn c') cmd.color('salmon','resn g') cmd.color('palegreen','resn t') cmd.color('paleyellow', 'resn u')\n''') points = points + 3 if points == 3: tkMessageBox.showinfo('Nucleic Acid Key','Adenine = light blue\nCytosine = orange\nGuanine = salmon red\nThymine = light green\nUracil = light yellow') else: tkMessageBox.showinfo("Error", "There is no DNA or RNA in this molecule.") # default view def std_view(self): try: self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.populate() cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.set('cartoon_ring_mode' ,'1') cmd.show('spheres','het') if self.script == '1': self.f.write('''cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.set('cartoon_ring_mode' ,'1') cmd.show('spheres','het')\n''') self.cpkligands() cmd.show('cartoon', 'resn a+t+g+c+u') cmd.color('limegreen','resn a+t+g+c+u') if self.script == '1': self.f.write('''cmd.show('cartoon', 'resn a+t+g+c+u') cmd.color('limegreen','resn a+t+g+c+u')\n''') except: self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.populate() cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.show('spheres','het') if self.script=='1': self.f.write('''cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.show('spheres','het')''') self.cpkligands() cmd.show('cartoon', 'resn a+t+g+c+u') cmd.color('limegreen','resn a+t+g+c+u') if self.script =='1': self.f.write('''cmd.show('cartoon', 'resn a+t+g+c+u') cmd.color('limegreen','resn a+t+g+c+u')\n''') # show hetero atoms def show_hetero(self): try: import tkMessageBox self.delcrea() cmd.remove('resn HOH') if self.script=='1': self.f.write('''cmd.remove('resn HOH')\n''') self.update(self.p) objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') self.checkitforthese() if 'ligands' in objects: self.set_defaults() if 'protein' in objects: cmd.show('cartoon', 'protein') cmd.set('cartoon_transparency','0.7','protein') if self.script=='1': self.f.write('''cmd.show('cartoon', 'protein') cmd.set('cartoon_transparency','0.7','protein')\n''') if 'nucleic_acid' in objects: cmd.set('cartoon_ring_mode', '1') cmd.show('cartoon','nucleic_acid') cmd.set('cartoon_transparency','0.7','nucleic_acid') cmd.color('cyan', 'nucleic_acid') if self.script=='1': self.f.write('''cmd.set('cartoon_ring_mode', '1') cmd.show('cartoon','nucleic_acid') cmd.set('cartoon_transparency','0.7','nucleic_acid') cmd.color('cyan', 'nucleic_acid')\n''') cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.1','ligands') cmd.show("sticks", "ligands around 6'") cmd.set('stick_radius','0.3','ligands around 6') cmd.color('orange','ligands') cmd.select("interaction","ligands around 6'") if self.script=='1': self.f.write('''cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.1','ligands') cmd.show("sticks", "ligands around 6'") cmd.set('stick_radius','0.3','ligands around 6') cmd.color('orange','ligands') cmd.select("interaction","ligands around 6'")\n''') self.cpkinteraction() cmd.set('stick_transparency', '0.1', 'interaction') cmd.disable('interaction') if self.script=='1': self.f.write('''cmd.set('stick_transparency', '0.1', 'interaction') cmd.disable('interaction')\n''') else: tkMessageBox.showinfo("Error", "There are no hetero atoms in this molecule.") except: import tkMessageBox self.delcrea() cmd.remove('resn HOH') if self.script =='1': self.f.write('''cmd.remove('resn HOH')\n''') self.update(self.p) objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') self.checkitforthese() if 'ligands' in objects: self.set_defaults() if 'protein' in objects: cmd.show('cartoon', 'protein') cmd.set('cartoon_transparency','0.7','protein') if self.script=='1': self.f.write('''cmd.show('cartoon', 'protein') cmd.set('cartoon_transparency','0.7','protein')\n''') if 'nucleic_acid' in objects: cmd.show('cartoon','nucleic_acid') cmd.set('cartoon_transparency','0.7','nucleic_acid') cmd.color('cyan', 'nucleic_acid') if self.script=='1': self.f.write('''cmd.show('cartoon','nucleic_acid') cmd.set('cartoon_transparency','0.7','nucleic_acid') cmd.color('cyan', 'nucleic_acid')\n''') cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.1','ligands') cmd.show("sticks", "ligands around 6'") cmd.set('stick_radius','0.3','ligands around 6') cmd.color('orange','ligands') cmd.select("interaction","ligands around 6'") if self.script=='1': self.f.write('''cmd.show('spheres','ligands') cmd.set('sphere_transparency','0.1','ligands') cmd.show("sticks", "ligands around 6'") cmd.set('stick_radius','0.3','ligands around 6') cmd.color('orange','ligands') cmd.select("interaction","ligands around 6'")\n''') self.cpkinteraction() cmd.set('stick_transparency', '0.1', 'interaction') cmd.disable('interaction') if self.script=='1': self.f.write('''cmd.set('stick_transparency', '0.1', 'interaction') cmd.disable('interaction')\n''') else: tkMessageBox.showinfo("Error", "There are no hetero atoms in this molecule.") # ball and stick view def ball_and_stick(self): self.update(self.p) objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') self.checkitforthese() self.set_defaults() self.delcrea() cmd.set("stick_radius","0.1","all") cmd.set("sphere_scale","0.3","all") if self.script=='1': self.f.write('''cmd.set("stick_radius","0.1","all") cmd.set("sphere_scale","0.3","all")\n''') if 'protein' in objects: cmd.show('spheres','protein') cmd.show('sticks','protein') if self.script=='1': self.f.write('''cmd.show('spheres','protein') cmd.show('sticks','protein')\n''') self.cpkprotein() if 'nucleic_acid' in objects: try: cmd.set('cartoon_ring_mode', '1') cmd.show('cartoon','resn a+g+c+t+u') cmd.show('spheres','resn a+g+c+t+u') cmd.show('sticks','resn a+g+c+t+u') if self.script=='1': self.f.write('''cmd.set('cartoon_ring_mode', '1') cmd.show('cartoon','resn a+g+c+t+u') cmd.show('spheres','resn a+g+c+t+u') cmd.show('sticks','resn a+g+c+t+u')\n''') self.cpknucleic() except: cmd.show('cartoon','resn a+g+c+t+u') if self.script=='1': self.f.write('''cmd.show('cartoon','resn a+g+c+t+u')\n''') self.cpknucleic() if 'ligands' in objects: cmd.show('spheres','ligands') cmd.color('orange', 'ligands') if self.script=='1': self.f.write('''cmd.show('spheres','ligands') cmd.color('orange', 'ligands')\n''') # show the surface of the molecule def surface_view(self): self.delcrea() self.update(self.p) objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') self.checkitforthese() self.set_defaults() cmd.show('surface','all') if self.script=='1': self.f.write(''' cmd.show('surface','all')\n''') self.cpkprotein() # show the polarities of the molecule def view_polarity(self): self.delcrea() self.update(self.p) self.checkitforthese() self.set_defaults() objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') if 'protein' in objects: cmd.show('surface', 'protein') if self.script=='1': self.f.write('''cmd.show('surface', 'protein')\n''') cmd.color('red','resn ALA+ILE+LEU+MET+PHE+PRO+TRP+VAL') cmd.color('blue','resn THR+SER+ARG+ASN+ASP+GLN+GLU+HIS+LYS') cmd.show('spheres','het') cmd.color('green','het') if self.script=='1': self.f.write('''cmd.color('red','resn ALA+ILE+LEU+MET+PHE+PRO+TRP+VAL') cmd.color('blue','resn THR+SER+ARG+ASN+ASP+GLN+GLU+HIS+LYS') cmd.show('spheres','het') cmd.color('green','het')\n''') try: cmd.set('cartoon_ring_mode' ,'1') if self.script=='1': self.f.write(''' cmd.set('cartoon_ring_mode' ,'1')\n''') except: cmd.color('green','het') if self.script=='1': self.f.write('''cmd.color('green','het')\n''') cmd.show('cartoon','resn a+g+c+t+u') if self.script=='1': self.f.write('''cmd.show('cartoon','resn a+g+c+t+u')\n''') self.cpknucleic() import tkMessageBox tkMessageBox.showinfo('Info', 'Red = Hydrophobic\nBlue = Hydrophilic') # putty representation def show_putty(self): try: self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() cmd.hide('all') cmd.show('spheres', 'het') cmd.color('orange', 'het') cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.cartoon('putty','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('sticks','resn t+g+c+a+u') if self.script=='1': self.f.write('''cmd.hide('all') cmd.show('spheres', 'het') cmd.color('orange', 'het') cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color("red", "ss h") cmd.color("yellow", "ss s") cmd.color("cyan", "ss l+\'\'") cmd.cartoon('putty','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('sticks','resn t+g+c+a+u')\n''') self.cpknucleic() except: import tkMessageBox tkMessageBox.showinfo('Error', 'Putty is not supported by this version of PyMol\nTry downloading the newest version to troubleshoot this problem') # aromatics view def color_aromatics(self): self.update(self.p) self.set_defaults() self.checkitforthese() self.delcrea() cmd.hide('all') cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color('aquamarine','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.set('cartoon_transparency','0.6','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('cartoon','resn t+u+g+c+a') cmd.color('aquamarine','resn u+g+c+a+t') cmd.set('cartoon_transparency','0.6','resn a+u+c+t+g') cmd.select('aromatics','resn phe+tyr+trp+his') cmd.color('red', 'aromatics') cmd.show('sticks','aromatics and (!name c+n+o)') cmd.set('stick_radius','0.4','all') cmd.delete('aromatics') if self.script=='1': self.f.write('''cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.color('aquamarine','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.set('cartoon_transparency','0.6','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('cartoon','resn t+u+g+c+a') cmd.color('aquamarine','resn u+g+c+a+t') cmd.set('cartoon_transparency','0.6','resn a+u+c+t+g') cmd.select('aromatics','resn phe+tyr+trp+his') cmd.color('red', 'aromatics') cmd.show('sticks','aromatics and (!name c+n+o)') cmd.set('stick_radius','0.4','all') cmd.delete('aromatics')\n''') cmd.deselect() # color the molecule by chain def color_by_chain(self): self.set_defaults() self.checkitforthese() self.delcrea() cmd.hide('all') cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('sticks','resn a+g+c+t+u') cmd.set('sphere_scale','0.4','resn u') cmd.color("blue","chain A") cmd.color("orange","chain B" ) cmd.color("silver","chain C") cmd.color("green","chain D") cmd.color("yellow","chain E") cmd.color("purple","chain F") cmd.color("grey","chain G") cmd.color("brown","chain H") cmd.color("slate","chain I") cmd.color("brightorange","chain J") cmd.color("lightblue","chain K" ) cmd.color("lightorange","chain L" ) cmd.color("purple","chain M" ) cmd.color("pink","chain N" ) cmd.color("forest","chain O" ) cmd.color("firebrick","chain P" ) cmd.color("paleyellow","chain Q" ) cmd.color("purpleblue","chain R" ) cmd.color("deepteal","chain S" ) cmd.color("deepolive","chain T" ) cmd.color("pink","chain U" ) cmd.color("salmon","chain V" ) cmd.color("ruby","chain W" ) cmd.color("wheat","chain X" ) cmd.color("lightmagenta","chain Y") cmd.color("aquamarine","chain Z") if self.script=='1': self.f.write('''cmd.hide('all') cmd.show('cartoon','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.show('sticks','resn a+g+c+t+u') cmd.set('sphere_scale','0.4','resn u') cmd.color("blue","chain A") cmd.color("orange","chain B" ) cmd.color("silver","chain C") cmd.color("green","chain D") cmd.color("yellow","chain E") cmd.color("purple","chain F") cmd.color("grey","chain G") cmd.color("brown","chain H") cmd.color("slate","chain I") cmd.color("brightorange","chain J") cmd.color("lightblue","chain K" ) cmd.color("lightorange","chain L" ) cmd.color("purple","chain M" ) cmd.color("pink","chain N" ) cmd.color("forest","chain O" ) cmd.color("firebrick","chain P" ) cmd.color("paleyellow","chain Q" ) cmd.color("purpleblue","chain R" ) cmd.color("deepteal","chain S" ) cmd.color("deepolive","chain T" ) cmd.color("pink","chain U" ) cmd.color("salmon","chain V" ) cmd.color("ruby","chain W" ) cmd.color("wheat","chain X" ) cmd.color("lightmagenta","chain Y") cmd.color("aquamarine","chain Z")\n''') #------------Brett's and Charlie's Code------------ #-------Show Charged------------------- def show_charged(self): self.delcrea() self.set_defaults() self.update(self.p) self.checkitforthese() objects = cmd.get_names('all') cmd.hide('everything') cmd.show('cartoon','all') cmd.color('gray','all') cmd.select('pos','resn arg+lys+his') cmd.show('sticks', 'pos and !name c+n+o') cmd.color('marine','pos') cmd.delete('pos') cmd.select('neg', 'resn glu+asp') cmd.show('sticks', 'neg and !name c+n+o') cmd.color('red','neg') cmd.delete('neg') cmd.set('cartoon_smooth_loops','0') if self.script=='1': self.f.write('''objects = cmd.get_names('all') cmd.hide('everything') cmd.show('cartoon','all') cmd.color('gray','all') cmd.select('pos','resn arg+lys+his') cmd.show('sticks', 'pos and !name c+n+o') cmd.color('marine','pos') cmd.delete('pos') cmd.select('neg', 'resn glu+asp') cmd.show('sticks', 'neg and !name c+n+o') cmd.color('red','neg') cmd.delete('neg') cmd.set('cartoon_smooth_loops','0')\n''') if 'protein' in objects: import tkMessageBox tkMessageBox.showinfo('Charge Info', 'Blue = Positively charged Amino Acids\nRed = Negatively charged Amino Acids') def surf_toon(self): self.delcrea() self.color_by_chain() cmd.hide('everything') cmd.show('cartoon','all') cmd.select('surface', 'all') cmd.do('show surface, all') cmd.do('set transparency, 0.5, surface') cmd.set('cartoon_smooth_loops','0') cmd.delete('surface') if self.script=='1': self.f.write('''cmd.hide('everything') cmd.show('cartoon','all') cmd.select('surface', 'all') cmd.do('show surface, all') cmd.do('set transparency, 0.5, surface') cmd.set('cartoon_smooth_loops','0') cmd.delete('surface')\n''') def surf_stick(self): self.delcrea() self.update(self.p) self.checkitforthese() cmd.hide('everything') cmd.show('stick','all') cmd.select('surface', 'all') cmd.do('show surface, all') cmd.do('set transparency, 0.5, surface') cmd.delete('surface') if self.script=='1': self.f.write(''' cmd.hide('everything') cmd.show('stick','all') cmd.select('surface', 'all') cmd.do('show surface, all') cmd.do('set transparency, 0.5, surface') cmd.delete('surface')\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() def mesh_stick(self): self.delcrea() cmd.hide('everything') cmd.do("show stick, all") cmd.do("color white, all") cmd.do("create mesh1, all") cmd.set('mesh_quality', '3') cmd.do("show mesh, mesh1") cmd.color('tv_blue', 'mesh1') cmd.hide("stick", "mesh1") if self.script=='1': self.f.write('''cmd.hide('everything') cmd.do("show stick, all") cmd.do("color white, all") cmd.do("create mesh1, all") cmd.set('mesh_quality', '3') cmd.do("show mesh, mesh1") cmd.color('tv_blue', 'mesh1') cmd.hide("stick", "mesh1")\n''') def stick_toon(self): self.delcrea() cmd.hide('everything') cmd.show('lines') cmd.create('cartoon', 'all') cmd.show('cartoon', 'cartoon') cmd.color('salmon', 'cartoon') cmd.color('cyan', 'resn a+t+u+g+c') if self.script=='1': self.f.write('''cmd.hide('everything') cmd.show('lines') cmd.create('cartoon', 'all') cmd.show('cartoon', 'cartoon') cmd.color('salmon', 'cartoon') cmd.color('cyan', 'resn a+t+u+g+c')\n''') def dot_line(self): self.delcrea() cmd.set('dot_density', '3') cmd.hide('everything') cmd.remove('resn HOH') cmd.hide('everything') cmd.show('lines') cmd.show('dots', 'all') if self.script=='1': self.f.write('''cmd.set('dot_density', '3') cmd.hide('everything') cmd.remove('resn HOH') cmd.hide('everything') cmd.show('lines') cmd.show('dots', 'all')\n''') def rovingstickers(self): self.update(self.p) self.checkitforthese() self.delcrea() cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set("stick_radius",0.3) cmd.set("roving_sticks",self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) if self.script=='1': self.f.write('''cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set("stick_radius",0.3) cmd.set("roving_sticks",self.rovingradius2.get()) cmd.set("roving_polar_contacts",8)\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() def rovinglines(self): self.update(self.p) self.checkitforthese() self.delcrea() cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set("roving_sticks",0) cmd.set('roving_lines', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) if self.script=='1': self.f.write('''cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set("roving_sticks",0) cmd.set('roving_lines', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8)\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() def rovingballstick(self): self.update(self.p) self.checkitforthese() self.delcrea() cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set('roving_sticks', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) cmd.set('roving_spheres', self.rovingradius2.get()) cmd.set('sphere_transparency', '0.2') cmd.set("stick_radius","0.1","all") cmd.set("sphere_scale","0.3","all") if self.script=='1': self.f.write('''cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set('roving_sticks', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) cmd.set('roving_spheres', self.rovingradius2.get()) cmd.set('sphere_transparency', '0.2') cmd.set("stick_radius","0.1","all") cmd.set("sphere_scale","0.3","all")\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() def rovingspheres(self): self.update(self.p) self.checkitforthese() cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set('roving_spheres', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) cmd.set('sphere_transparency', '0.2') cmd.set('sphere_scale', '0.8', 'all') if self.script=='1': self.f.write('''cmd.hide('everything') cmd.remove("hydro") cmd.set("roving_detail",1) cmd.set("roving_origin",1) cmd.set('roving_spheres', self.rovingradius2.get()) cmd.set("roving_polar_contacts",8) cmd.set('sphere_transparency', '0.2') cmd.set('sphere_scale', '0.8', 'all')\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() def chain_contact(self): self.delcrea() cmd.hide('everything') cmd.show('mesh', 'all') cmd.color('gray40', 'all') cmd.select("Chain-A", "chain A") cmd.select("Chain-B", "chain B") cmd.select("Chain-C", "chain C") cmd.select("Chain-D", "chain D") cmd.select("Chain-E", "chain E") cmd.select("Chain-F", "chain F") cmd.select("Chain-G", "chain G") cmd.select("Chain-H", "chain H") cmd.select("Chain-I", "chain I") cmd.select("Chain-J", "chain J") cmd.select("Chain-K", "chain K") cmd.select("Chain-L", "chain L") cmd.select("Chain-M", "chain M") cmd.select("Chain-N", "chain N") cmd.select("Chain-O", "chain O") cmd.select("Chain-P", "chain P") cmd.select("Chain-Q", "chain Q") cmd.select("Chain-R", "chain R") cmd.select("Chain-S", "chain S") cmd.select("Chain-T", "chain T") cmd.select("Chain-U", "chain U") cmd.select("Chain-V", "chain V") cmd.select("Chain-W", "chain W") cmd.select("Chain-X", "chain X") cmd.select("Chain-Y", "chain Y") cmd.select("Chain-Z", "chain Z") self.checkforchain() cmd.orient() objects = cmd.get_names('all') chainpulllist = [] if 'Chain-A' in objects: chainpulllist.append('Chain-A') if 'Chain-B' in objects: chainpulllist.append('Chain-B') if 'Chain-C' in objects: chainpulllist.append('Chain-C') if 'Chain-D' in objects: chainpulllist.append('Chain-D') if 'Chain-E' in objects: chainpulllist.append('Chain-E') if 'Chain-F' in objects: chainpulllist.append('Chain-F') if 'Chain-G' in objects: chainpulllist.append('Chain-G') if 'Chain-H' in objects: chainpulllist.append('Chain-H') if 'Chain-I' in objects: chainpulllist.append('Chain-I') if 'Chain-J' in objects: chainpulllist.append('Chain-J') if 'Chain-K' in objects: chainpulllist.append('Chain-K') if 'Chain-L' in objects: chainpulllist.append('Chain-L') if 'Chain-M' in objects: chainpulllist.append('Chain-M') if 'Chain-N' in objects: chainpulllist.append('Chain-N') if 'Chain-O' in objects: chainpulllist.append('Chain-O') if 'Chain-P' in objects: chainpulllist.append('Chain-P') if 'Chain-Q' in objects: chainpulllist.append('Chain-Q') if 'Chain-R' in objects: chainpulllist.append('Chain-R') if 'Chain-S' in objects: chainpulllist.append('Chain-S') if 'Chain-T' in objects: chainpulllist.append('Chain-T') if 'Chain-U' in objects: chainpulllist.append('Chain-U') if 'Chain-V' in objects: chainpulllist.append('Chain-V') if 'Chain-W' in objects: chainpulllist.append('Chain-W') if 'Chain-X' in objects: chainpulllist.append('Chain-X') if 'Chain-Y' in objects: chainpulllist.append('Chain-Y') if 'Chain-Z' in objects: chainpulllist.append('Chain-Z') if len(chainpulllist) >1: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >2: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[3]) cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >2: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') def show_cpk(self): self.update(self.p) objects = cmd.get_names('all') if self.script=='1': self.f.write('''objects = cmd.get_names('all')\n''') self.checkitforthese() self.set_defaults() self.delcrea() cmd.set("sphere_scale","0.7","all") cmd.show('spheres','all') if self.script=='1': self.f.write('''cmd.set("sphere_scale","0.7","all") cmd.show('spheres','all')\n''') self.cpkprotein()#stopped here self.cpkligands() self.cpknucleic() def spheresurf(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() cmd.show('spheres', 'all') cmd.create('surface', 'all') cmd.show('surface', 'surface') cmd.color('white', 'surface') cmd.set('sphere_scale', '0.5', 'all') cmd.set('transparency', '0.4') if self.script=='1': self.f.write('''cmd.show('spheres', 'all') cmd.create('surface', 'all') cmd.show('surface', 'surface') cmd.color('white', 'surface') cmd.set('sphere_scale', '0.5', 'all') cmd.set('transparency', '0.4')\n''') self.cpkprotein() self.cpknucleic() self.cpkligands() #-----------Electron Density Presets----------------# def mesh_ribbon(self): try: self.delcrea() try: cmd.hide('everything') cmd.isomesh('map1','map', contour1.get()) if self.script=='1': self.f.write('''cmd.hide('everything') cmd.isomesh('map1','map', contour1.get())\n''') except: try: cmd.set("suspend_updates",1,quiet=1) cmd.remove("hydro") cmd.map_new('map',"gaussian","0.75", 'all') cmd.set("suspend_updates",0,quiet=1) cmd.refresh() cmd.isomesh('map1','map', '1') if self.script=='1': self.f.write('''cmd.set("suspend_updates",1,quiet=1) cmd.remove("hydro") cmd.map_new('map',"gaussian","0.75", 'all') cmd.set("suspend_updates",0,quiet=1) cmd.refresh() cmd.isomesh('map1','map', '1')\n''') except: import tkMessageBox tkMessageBox.showinfo("Error", 'No PDB is present') cmd.show('ribbon', 'all') cmd.show('lines', 'all') cmd.color('red', 'all') cmd.color('purpleblue', 'map1') if self.script=='1': self.f.write('''cmd.show('ribbon', 'all') cmd.show('lines', 'all') cmd.color('red', 'all') cmd.color('purpleblue', 'map1')\n''') except: cmd.show('lines', 'all') if self.script=='1': self.f.write('''cmd.show('lines', 'all')''') import tkMessageBox tkMessageBox.showinfo('Alert', 'Protein must be present') def dot_sticks(self): try: self.delcrea() cmd.hide('everything') if self.script=='1': self.f.write('''cmd.hide('everything')\n''') try: cmd.set("suspend_updates",1,quiet=1) cmd.remove("hydro") cmd.enable('all') cmd.map_new('map',"gaussian","0.75", 'all') cmd.isodot("map1", "map", 9999.0, 'all') cmd.set("suspend_updates",0,quiet=1) cmd.refresh() cmd.isodot('map1','map', '1') if self.script=='1': self.f.write('''cmd.set("suspend_updates",1,quiet=1) cmd.remove("hydro") cmd.enable('all') cmd.map_new('map',"gaussian","0.75", 'all') cmd.isodot("map1", "map", 9999.0, 'all') cmd.set("suspend_updates",0,quiet=1) cmd.refresh() cmd.isodot('map1','map', '1')\n''') except: import tkMessageBox tkMessageBox.showinfo("Error", 'No PDB is present') cmd.show('sticks', 'all') cmd.color('blue', 'all') cmd.color('red', 'map1') if self.script=='1': self.f.write('''cmd.show('sticks', 'all') cmd.color('blue', 'all') cmd.color('red', 'map1')\n''') except: cmd.show('lines', 'all') if self.script=='1': self.f.write('''cmd.show('lines', 'all')\n''') import tkMessageBox tkMessageBox.showinfo('Alert', 'Protein must be present') def surfinglines(self): try: cmd.hide('everything') if self.script=='1': self.f.write('''cmd.hide('everything')\n''') self.update(self.p) self.checkitforthese() self.delcrea() try: cmd.remove("hydro") cmd.map_new('map',"gaussian","0.75", 'all') cmd.isosurface('map1','map','1') cmd.show('lines', 'all') self.cpkprotein() self.cpkligands() self.cpknucleic() cmd.color('white', 'elem c') cmd.color('orange', "map1") cmd.set('transparency', '0.4') cmd.set('ambient', '0.45') if self.script=='1': self.f.write('''cmd.remove("hydro") cmd.map_new('map',"gaussian","0.75", 'all') cmd.isosurface('map1','map','1') cmd.show('lines', 'all') self.cpkprotein() self.cpkligands() self.cpknucleic() cmd.color('white', 'elem c') cmd.color('orange', "map1") cmd.set('transparency', '0.4') cmd.set('ambient', '0.45')\n''') except: cmd.show('lines', 'all') if self.script=='1': self.f.write('''cmd.show('lines', 'all')\n''') import tkMessageBox tkMessageBox.showinfo("Error", 'No PDB is present') except: cmd.show('lines', 'all') if self.script=='1': self.f.write('''cmd.show('lines', 'all')\n''') import tkMessageBox tkMessageBox.showinfo('Alert', 'Protein must be present') #------------------Motif stuff--------------------- def deletemotif(self): cmd.delete('p-loop') cmd.delete('serineprotease') cmd.delete('lactamase') cmd.delete('superoxide') cmd.delete('metalloprotease') cmd.delete('tyrophos') cmd.delete('carbonicanhydrase') cmd.delete('paplike') cmd.delete('Zinc_finger') cmd.delete('Aminotransferase') cmd.delete('fucoseisomerase') cmd.delete('Ligase') cmd.delete('o-glycosyl') cmd.delete('glu_amidotransferase') cmd.delete('Peroxidase') cmd.delete('carboncarbon') cmd.delete('Tkinase') cmd.delete('TrioseIsomerase') cmd.delete('alcoholdehyd') cmd.delete('Cis-trans') cmd.delete('aldoreductase') cmd.delete('NAD-reductase') cmd.delete('NAD-reductase2') cmd.delete('chondroitinase') cmd.delete('Hyaluronate_Lyase') cmd.delete('deacetylase') cmd.delete('p-loop') cmd.delete('adenylatekinase') cmd.delete('SRC-Kinase') cmd.delete('Cyclin_Kinase') cmd.delete('Serotonin_transferase') cmd.delete('actase') cmd.delete('Exonuclease3') cmd.delete('Citrate_Synth') cmd.delete('hhal') cmd.delete('betaine_dehydrogenase') #----------Motif definitions consisting of measuring atom to atom between different # amino acid residues and allowing them to be altered by a slider def serineprotease(self): self.update(self.p)#updates list of molecular groups objects = cmd.get_names('all')#gets names of objects self.checkitforthese()#sees if objects are in objects self.set_defaults()#sets defaults self.delcrea()#deletes created objects self.deletemotif()#deletes previous motif cmd.select('asp1', 'resn asp within %s of resn his' %(self.range.get()*3)) #selects aspartate within 3 of histidine cmd.select('asp2', 'resn asp within %s of resn ser'%(self.range.get()*7)) cmd.select('asp', 'byres asp1 and byres asp2') cmd.select('his1', 'resn his within %s of asp' %(self.range.get()*4)) cmd.select('his2', 'resn his within %s of resn ser' %(self.range.get()*4)) cmd.select('his', 'byres his1 and byres his2') cmd.select('ser1', 'name og within %s of name ne2' %(self.range.get()*3.5)) cmd.select('ser2', 'resn ser within %s of asp' %(self.range.get()*7)) cmd.select('ser', 'byres ser1 and byres ser2') cmd.select('serineprotease', 'ser(his(asp))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'serineprotease') cmd.set('stick_radius','0.5') self.cpkserineprotease()#colors in cpk cmd.orient('serineprotease') cmd.deselect()#deselects cmd.delete('asp')#delets selections cmd.delete('his') cmd.delete('ser') cmd.delete('asp1') cmd.delete('his1') cmd.delete('ser1') cmd.delete('asp2') cmd.delete('his2') cmd.delete('ser2') def Blactamase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('lys1', 'name nz and resn lys within %s of (name oh and resn tyr)' %(self.range.get()*5)) cmd.select('lys2', 'name nz and resn lys within %s of (name cz and resn tyr)' %(self.range.get()*5.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name ce1 and resn tyr)' %(self.range.get()*6.5)) cmd.select('lys4', 'name nz and resn lys within %s of (name ce2 and resn tyr)' %(self.range.get()*6.5)) cmd.select('lys5', 'name ce and resn lys within %s of (name oh and resn tyr)' %(self.range.get()*5)) cmd.select('lys6', 'name ce and resn lys within %s of (name cz and resn tyr)' %(self.range.get()*6)) cmd.select('lys7', 'name nz and resn lys within %s of (name og and resn ser)' %(self.range.get()*6)) cmd.select('lys8', 'name nz and resn lys within %s of (name cb and resn ser)' %(self.range.get()*5.2)) cmd.select('lys9', 'name cb and resn lys within %s of (name cb and resn ser)' %(self.range.get()*9.2)) cmd.select('lys10', 'name ce and resn lys within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('lys11', 'name nz and resn lys within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('lys12', 'name nz and resn lys within %s of (name oe2 and resn glu)' %(self.range.get()*12.5)) cmd.select('lys13', 'name ce and resn lys within %s of (name cd and resn glu)' %(self.range.get()*11)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13') cmd.select('tyr1', 'name oh and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*5)) cmd.select('tyr2', 'name cz and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*5.5)) cmd.select('tyr3', 'name ce1 and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*6.5)) cmd.select('tyr4', 'name ce2 and resn tyr within %s of (name nz and lys)' %(self.range.get()*6.5)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ce and resn lys)' %(self.range.get()*5)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name ce and resn lys)' %(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name og and resn ser)' %(self.range.get()*6)) cmd.select('tyr8', 'name cz and resn tyr within %s of (name og and resn ser)' %(self.range.get()*6.5)) cmd.select('tyr9', 'name oh and resn tyr within %s of (name cb and resn ser)' %(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name oe1 and resn glu)' %(self.range.get()*10)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name oe2 and resn glu)' %(self.range.get()*10)) cmd.select('tyr12', 'name oh and resn tyr within %s of (name cd and resn glu)' %(self.range.get()*10)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12') cmd.select('ser1', 'name cb and resn ser within %s of (name nz and resn lys)' %(self.range.get()*6)) cmd.select('ser2', 'name og and resn ser within %s of (name nz and resn lys)' %(self.range.get()*6)) cmd.select('ser3', 'name cb and resn ser within %s of (name cb and lys)' %(self.range.get()*8.2)) cmd.select('ser4', 'name og and resn ser within %s of (name cz and resn tyr)' %(self.range.get()*6.5)) cmd.select('ser5', 'name cb and resn ser within %s of (name oh and resn tyr)' %(self.range.get()*6.5)) cmd.select('ser6', 'name og and resn ser within %s of (name oh and tyr)' %(self.range.get()*6)) cmd.select('ser7', 'name og and resn ser within %s of (name oe1 and resn glu)' %(self.range.get()*12)) cmd.select('ser8', 'name og and resn ser within %s of (name oe2 and resn glu)' %(self.range.get()*12)) cmd.select('ser9', 'name cb and resn ser within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('ser10', 'name cb and resn ser within %s of (name oe2 and resn glu)' %(self.range.get()*12.5)) cmd.select('ser11', 'name og and resn ser within %s of (name cd and resn glu)' %(self.range.get()*12.5)) cmd.select('ser12', 'name cb and resn ser within %s of (name cd and resn glu)' %(self.range.get()*11.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10 and byres ser11 and byres ser12') cmd.select('glu1', 'name oe1 and resn glu within %s of (name ce and resn lys)' %(self.range.get()*8.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)' %(self.range.get()*9.5)) cmd.select('glu3', 'name oe2 and resn glu within %s of (name nz and lys)' %(self.range.get()*11.2)) cmd.select('glu4', 'name cd and resn glu within %s of (name ce and resn lys)' %(self.range.get()*10.6)) cmd.select('glu5', 'name oe1 and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*8.7)) cmd.select('glu6', 'name oe2 and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*9.7)) cmd.select('glu7', 'name cd and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*9.6)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name og and resn ser)' %(self.range.get()*10.5)) cmd.select('glu9', 'name oe2 and resn glu within %s of (name og and resn ser)' %(self.range.get()*10.5)) cmd.select('glu10', 'name oe1 and resn glu within %s of (name cb and resn ser)' %(self.range.get()*10)) cmd.select('glu11', 'name oe2 and resn glu within %s of (name cb and resn ser)' %(self.range.get()*11.8)) cmd.select('glu12', 'name cd and resn glu within %s of (name og and resn ser)' %(self.range.get()*11.8)) cmd.select('glu13', 'name cd and resn glu within %s of (name cb and ser)' %(self.range.get()*11)) cmd.select('glu14', 'name oe1 and resn glu within %s of (name cg and tyr)' %(self.range.get()*7.4)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11 and byres glu12 and byres glu13 and byres glu14') cmd.select('lactamase', 'ser(tyr(glu(lys)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.8', 'all') cmd.show('sticks', 'lactamase') cmd.set('stick_radius','0.5') self.cpkBlactamase() cmd.orient('lactamase') cmd.deselect cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr2') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser11') cmd.delete('ser12') cmd.delete('ser') cmd.delete('glu') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu12') cmd.delete('glu13') cmd.delete('glu14') cmd.deselect() def superoxide(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'byres resn his within %s of elem cu'%(self.range.get()*4)) cmd.select('arg1', 'byres resn arg within %s of elem cu'%(self.range.get()*6)) cmd.select('stuff', 'his1 and (byres elem zn around %s)'%(self.range.get()*4)) cmd.select('stuff1', 'arg1 and (byres elem zn around %s)'%(self.range.get()*6)) cmd.select('stuff2', 'byres elem cu around %s and his1'%(self.range.get()*4)) cmd.select('stuff3', 'byres elem cu around %s and arg1'%(self.range.get()*6)) cmd.select('stuff4', 'stuff and stuff1 and stuff2 and stuff3') cmd.select('superoxide', 'byres his1(arg1(stuff4))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.show('sticks', 'superoxide') cmd.color('copper', 'elem cu') cmd.color('grey40', 'elem zn') cmd.show('spheres', 'elem cu') cmd.show('spheres', 'elem zn') cmd.set('cartoon_transparency', '0.7', 'all') self.cpkreductase() cmd.deselect() cmd.orient('superoxide') cmd.delete('his1') cmd.delete('arg1') cmd.delete('stuff') cmd.delete('stuff1') cmd.delete('stuff2') cmd.delete('stuff3') cmd.delete('stuff4') def metalloprotease(self): self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.hide('everything') cmd.select('zn', 'elem zn') cmd.show('sphere', 'zn') cmd.select('metalloprotease', 'zn(byres zn around %s)'%(self.range.get()*5)) cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'metalloprotease') self.cpkmetalloprotease() cmd.delete('zn') cmd.orient('metalloprotease') cmd.deselect() def tyrophos(self): self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.hide('everything') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('arg3', 'name ne and resn arg within %s of (name cb and resn asp)'%(self.range.get()*6.5)) cmd.select('arg4', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*7)) cmd.select('arg5', 'name nh1 and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg6', 'name ne and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name og and resn ser)'%(self.range.get()*10)) cmd.select('arg8', 'name nh1 and resn arg within %s of (name cb and resn ser)'%(self.range.get()*11.2)) cmd.select('arg9', 'name ne and resn arg within %s of (name ca and resn ser)'%(self.range.get()*9)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg6 and byres arg7 and byres arg8 and byres arg9') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh1 and arg)'%(self.range.get()*7)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('asp3', 'name cb and resn asp within %s of (name ne and arg)'%(self.range.get()*6.5)) cmd.select('asp4', 'name od2 and resn asp within %s of (name c and resn ser)'%(self.range.get()*11)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ca and resn ser)'%(self.range.get()*12)) cmd.select('asp6', 'name cb and resn asp within %s of (name cb and resn ser)'%(self.range.get()*9.2)) cmd.select('asp7', 'name od1 and resn asp within %s of (name c and resn cys)'%(self.range.get()*12)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*11)) cmd.select('asp9', 'name cb and resn asp within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('cys1', 'name ca and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys3', 'name sg and resn cys within %s of (name ca and resn ser)'%(self.range.get()*6)) cmd.select('cys4', 'name c and resn cys within %s of (name od1 and asp)'%(self.range.get()*12)) cmd.select('cys5', 'name cb and resn cys within %s of (name od2 and asp)'%(self.range.get()*11)) cmd.select('cys6', 'name sg and resn cys within %s of (name cb and asp)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name nh1 and arg)'%(self.range.get()*7)) cmd.select('cys9', 'name sg and resn cys within %s of (name ne and arg)'%(self.range.get()*6.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name nh2 and arg)'%(self.range.get()*10)) cmd.select('ser2', 'name cb and resn ser within %s of (name nh1 and arg)'%(self.range.get()*11.2)) cmd.select('ser3', 'name ca and resn ser within %s of (name ne and arg)'%(self.range.get()*9)) cmd.select('ser4', 'name c and resn ser within %s of (name od2 and asp)'%(self.range.get()*11)) cmd.select('ser5', 'name ca and resn ser within %s of (name od1 and asp)'%(self.range.get()*12)) cmd.select('ser6', 'name cb and resn ser within %s of (name cb and asp)'%(self.range.get()*9.2)) cmd.select('ser7', 'name og and resn ser within %s of (name ca and cys)'%(self.range.get()*6.5)) cmd.select('ser8', 'name cb and resn ser within %s of (name cb and cys)'%(self.range.get()*7)) cmd.select('ser9', 'name ca and resn ser within %s of (name sg and cys)'%(self.range.get()*6)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('tyrophos', 'ser(asp(arg(cys)))') tycount = cmd.index('tyrophos') atcount = len(tycount) if(atcount < 1): cmd.hide('everything') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('arg3', 'name ne and resn arg within %s of (name cb and resn asp)'%(self.range.get()*6.5)) cmd.select('arg4', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*7)) cmd.select('arg5', 'name nh1 and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg6', 'name ne and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg6') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh1 and resn arg)'%(self.range.get()*7)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*7)) cmd.select('asp3', 'name cb and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name c and resn cys)'%(self.range.get()*12)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*11)) cmd.select('asp9', 'name cb and resn asp within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp7 and byres asp8 and byres asp9') cmd.select('cys4', 'name c and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*12)) cmd.select('cys5', 'name cb and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*11)) cmd.select('cys6', 'name sg and resn cys within %s of (name cb and resn asp)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name nh2 and resn arg)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name nh1 and resn arg)'%(self.range.get()*7)) cmd.select('cys9', 'name sg and resn cys within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('cys', 'byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('tyrophos', '(asp(arg(cys)))') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'tyrophos') cmd.hide('cartoon', 'tyrophos') self.cpktyrophos() cmd.delete('arg') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.orient('tyrophos') cmd.deselect() else: cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'tyrophos') cmd.hide('cartoon', 'tyrophos') self.cpktyrophos() cmd.delete('arg') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.orient('tyrophos') cmd.deselect() def carbanhyd(self): self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.hide('everything') cmd.select('zn', 'elem zn') cmd.select('his', 'resn his within %s of zn'%(self.range.get()*5)) cmd.select('carbonicanhydrase', 'byres his or zn') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'carbonicanhydrase') cmd.show('spheres', 'zn') self.cpkcarbanhyd() cmd.delete('zn') cmd.delete('his') cmd.orient('carbonicanhydrase') cmd.deselect() def paplike(self): self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.hide('everything') cmd.select('gln1', 'name ne2 and resn gln within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('gln2', 'name cd and resn gln within %s of (name ce1 and resn his)'%(self.range.get()*6.7)) cmd.select('gln3', 'name oe1 and resn gln within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('gln4', 'name ne2 and resn gln within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('gln5', 'name oe1 and resn gln within %s of (name sg and resn cys)'%(self.range.get()*6.7)) cmd.select('gln', 'byres gln1 and byres gln2 and byres gln3 and byres gln4 and byres gln5') cmd.select('his1', 'name ne2 and resn his within %s of (name ne2 and gln)'%(self.range.get()*7)) cmd.select('his2', 'name ce1 and resn his within %s of (name cd and gln)'%(self.range.get()*6.7)) cmd.select('his3', 'name nd1 and resn his within %s of (name oe1 and gln)'%(self.range.get()*7)) cmd.select('his4', 'name ce1 and resn his within %s of (name cb and resn cys)'%(self.range.get()*5.7)) cmd.select('his5', 'name nd1 and resn his within %s of (name sg and resn cys)'%(self.range.get()*6)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5') cmd.select('cys1', 'name cb and resn cys within %s of (name ce1 and his)'%(self.range.get()*5.7)) cmd.select('cys2', 'name sg and resn cys within %s of (name nd1 and his)'%(self.range.get()*6)) cmd.select('cys3', 'name cb and resn cys within %s of (name ne2 and gln)'%(self.range.get()*5.5)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe1 and gln)'%(self.range.get()*6.7)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4') cmd.select('paplike', 'gln(his(cys))') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'paplike') self.cpkpaplike() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('gln') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln4') cmd.delete('gln5') cmd.orient('paplike') cmd.deselect() def zincfinger(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('zn1', 'elem zn') xm = cmd.index('zn1') nm = len(xm) if(nm < 1): cmd.delete('zn1') objects = cmd.get_names('all') if 'zn1' in objects: cmd.select('zn1', 'elem zn') cmd.select('his', 'resn his') cmd.select('cys', 'resn cys') cmd.select('cys1', 'resn cys around %s'%(self.range.get()*4)) cmd.select('Zinc_finger', '(resn cys or resn his(and byres cys1))') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.color('white', 'all') cmd.show('sticks', 'Zinc_finger') cmd.show('spheres', 'elem zn') cmd.color('grey40', 'elem zn') self.cpkzincfinger() cmd.delete('zn1') cmd.delete('his') cmd.delete('cys') cmd.delete('cys1') cmd.orient('Zinc_finger') cmd.deselect() else: cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') def aminotransferase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('asp1', 'name od1 and resn asp within %s of (name cb and resn his)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name cg and resn his)'%(self.range.get()*6)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('asp4', 'name cg and resn asp within %s of (name cb and resn his)'%(self.range.get()*6.5)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asp6', 'name od1 and resn asp within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asp7', 'name od2 and resn asp within %s of (name nz and resn lys)'%(self.range.get()*9)) cmd.select('asp8', 'name cg and resn asp within %s of (name nz and resn lys)'%(self.range.get()*9)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp8') cmd.select('his1', 'name cb and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('his2', 'name cg and resn his within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('his3', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('his4', 'name cb and resn his within %s of (name cg and asp)'%(self.range.get()*6.5)) cmd.select('his5', 'name ne2 and resn his within %s of (name od1 and asp)'%(self.range.get()*8)) cmd.select('his6', 'name cd2 and resn his within %s of (name od1 and asp)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*8)) cmd.select('his9', 'name ce1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('lys1', 'name nz and resn lys within %s of (name od2 and asp)'%(self.range.get()*9)) cmd.select('lys2', 'name nz and resn lys within %s of (name cg and asp)'%(self.range.get()*9)) cmd.select('lys3', 'name nz and resn lys within %s of (name nd1 and his)'%(self.range.get()*7.5)) cmd.select('lys4', 'name nz and resn lys within %s of (name ne2 and his)'%(self.range.get()*8)) cmd.select('lys5', 'name nz and resn lys within %s of (name ce1 and his)'%(self.range.get()*7)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5') cmd.select('Aminotransferase', 'asp(his(lys))') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.show('sticks', 'Aminotransferase') self.cpkaminotransferase() cmd.orient('Aminotransferase') cmd.set('cartoon_transparency', '0.6', 'all') cmd.deselect() cmd.delete('his') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('lys') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') def fisomerase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his', 'elem mn around %s(elem mn)'%(self.range.get()*5)) cmd.select('fucoseisomerase', 'byres resn asp and his(byres resn glu and his(elem mn))') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.show('sticks', 'fucoseisomerase') cmd.show('spheres', 'elem mn') cmd.orient('fucoseisomerase') self.cpkfucoseisomerase() cmd.set('cartoon_transparency', '0.6', 'all') cmd.deselect() cmd.delete('his') def glutamine_amidotransferase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'name ND1 within %s of name OE2'%(self.range.get()*3)) cmd.select('his2', 'name NE2 within %s of name SG'%(self.range.get()*3.5)) cmd.select('his', 'byres his1 and byres his2') cmd.select('glu1', 'resn glu within %s of his'%(self.range.get()*3.2)) cmd.select('glu2', 'resn glu within %s of resn cys'%(self.range.get()*7)) cmd.select('glu', 'byres glu1 and byres glu2') cmd.select('cys1', 'resn cys within %s of his'%(self.range.get()*3.5)) cmd.select('cys2', 'resn cys within %s of glu'%(self.range.get()*7)) cmd.select('cys', 'byres cys1 and byres cys2') cmd.select('glu_amidotransferase', 'cys(his(glu))') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.show('sticks', 'glu_amidotransferase') cmd.orient('glu_amidotransferase') self.cpkglu_amidotransferase() cmd.set('cartoon_transparency', '0.6', 'all') cmd.deselect() cmd.delete('his') cmd.delete('his1') cmd.delete('his2') cmd.delete('glu') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') def dnaligase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('amp1', 'resn amp') cmd.select('atp1', 'resn atp') ######## xp = cmd.index('amp1') np = len(xp) if(np < 1):#-------------------looks to see if amp in objects and cmd.delete('amp1') ######## xtp = cmd.index('atp1') ntp = len(xtp) if(ntp < 1): cmd.delete('atp1') objects = cmd.get_names('all') if 'amp1' in objects: cmd.select('ramp1', 'byres resn amp around %s'%(self.range.get()*7.4)) cmd.select('lys1', 'byres resn lys and ramp1') cmd.select('ramp2', 'byres resn amp around %s'%(self.range.get()*7)) cmd.select('ramp3', 'byres resn amp around %s'%(self.range.get()*5.3)) cmd.select('asp1', 'ramp3 and(byres resn asp within %s of lys1)'%(self.range.get()*3)) cmd.select('arg1', 'ramp2 and(byres resn arg within %s of asp1)'%(self.range.get()*5)) cmd.select('Ligase', 'byres lys1(amp1(byres arg1(byres asp1)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Ligase') self.cpkdnaligase() cmd.deselect() elif 'atp1' in objects: cmd.select('ratp1', 'byres resn atp around %s'%(self.range.get()*7.4)) cmd.select('lys1', 'byres resn lys and ratp1') cmd.select('ratp2', 'byres resn atp around %s'%(self.range.get()*7)) cmd.select('ratp3', 'byres resn atp around %s'%(self.range.get()*5.3)) cmd.select('asp1', 'ratp3 and(byres resn asp within %s of lys1)'%(self.range.get()*3)) cmd.select('arg1', 'ratp2 and(byres resn arg within %s of asp1)'%(self.range.get()*5)) cmd.select('Ligase', 'byres lys1(atp1(byres arg1(byres asp1)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Ligase') self.cpkdnaligase() cmd.deselect() elif 'amp1' or 'atp1' not in objects: cmd.select('asp1', 'name OD2 within %s of name NE'%(self.range.get()*5.5)) cmd.select('arg1', 'name NE within %s of name OD2'%(self.range.get()*5.5)) cmd.select('lys1', 'name NZ within %s of name OD2'%(self.range.get()*9)) cmd.select('lys4', 'name NZ within %s of name NH2'%(self.range.get()*10)) cmd.select('arg', 'byres resn arg and arg1') cmd.select('asp', 'byres resn asp and asp1') cmd.select('lys3', 'byres resn lys and lys1 and lys4') cmd.select('Ligase', 'byres arg(asp(lys3))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Ligase') self.cpkdnaligase() cmd.deselect() cmd.orient('Ligase') cmd.delete('asp1') cmd.delete('arg1') cmd.delete('lys1') cmd.delete('arg') cmd.delete('asp') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys') cmd.delete('ratp1') cmd.delete('ratp2') cmd.delete('ratp3') cmd.delete('atp1') cmd.delete('ramp1') cmd.delete('ramp2') cmd.delete('ramp3') cmd.delete('lys') cmd.delete('amp1') def thymidinekinase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('glu1', 'name OE1 and resn glu within %s of name NH2 and resn arg'%(self.range.get()*5)) cmd.select('glu2', 'resn glu and name OE2 within %s of name NE and resn arg'%(self.range.get()*5)) cmd.select('glu3', 'resn glu and name OE1 within %s of name NH1 and resn arg'%(self.range.get()*6)) cmd.select('glu4', 'resn glu and name OE1 within %s of name NE and resn arg'%(self.range.get()*6)) cmd.select('glu5', 'resn glu and name OE2 within %s of name NH2 and resn arg'%(self.range.get()*5.5)) cmd.select('glu6', 'resn glu and name oe1 within %s of name CZ and resn arg'%(self.range.get()*5)) cmd.select('glu7', 'resn glu and name oe2 within %s of name CZ and resn arg'%(self.range.get()*5)) cmd.select('glu8', 'resn glu and name oe1 within %s of name CD and resn arg'%(self.range.get()*5.8)) cmd.select('glu9', 'resn glu and name oe2 within %s of name CD and resn arg'%(self.range.get()*5.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres resn glu') cmd.select('arg1', 'resn arg and name NH1 within %s of name OE2 and glu'%(self.range.get()*6)) cmd.select('arg2', 'resn arg and name NE within %s of name OE2 and glu'%(self.range.get()*5.2)) cmd.select('arg3', 'resn arg and name NH1 within %s of name oe1 and glu'%(self.range.get()*6)) cmd.select('arg4', 'resn arg and name ne within %s of name oe1 and resn glu'%(self.range.get()*6.5)) cmd.select('arg5', 'resn arg and name nh2 within %s of name oe2 and resn glu'%(self.range.get()*5.8)) cmd.select('arg', 'byres resn arg and byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5') cmd.select('gly1', 'byres resn gly within %s of arg'%(self.range.get()*6.2)) cmd.select('gly2', 'byres resn gly within %s of glu'%(self.range.get()*9)) cmd.select('gly', 'byres resn gly and byres gly1 and byres gly2') cmd.select('glu10', 'byres glu within 10 of gly') cmd.select('arg10', 'byres arg within 9 of gly') cmd.select('Tkinase', 'glu10(arg10(gly))') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Tkinase') self.cpkkinase() cmd.deselect() cmd.orient('Tkinase') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg10') cmd.delete('arg') cmd.delete('gly1') cmd.delete('gly2') cmd.delete('gly') cmd.delete('thm1') cmd.delete('tmp1') cmd.delete('tdp1') cmd.delete('ttp1') def oglycosyl(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('asp1', 'name od1 and resn asp within %s of (name oe1 and resn glu)'%(self.range.get()*9.5)) cmd.select('notasp', 'resn asp within %s of resn glu'%(4.5/self.range.get())) cmd.select('asp', 'asp1 and (byres not notasp)') cmd.select('glu1', 'name oe1 and resn glu within %s of (name od1 and resn asp)'%(self.range.get()*9.5)) cmd.select('glu0', 'resn glu within %s of resn asp'%(4.5/self.range.get())) cmd.select('glu', 'byres glu1 and (not glu0)') cmd.select('o-glycosyl', 'byres asp | byres glu') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'o-glycosyl') cmd.delete('tyr') cmd.delete('glu') cmd.delete('notasp') cmd.delete('glu1') cmd.delete('glu0') cmd.delete('asp1') cmd.delete('asp') cmd.orient('o-glycosyl') self.cpkoglycosyl() cmd.deselect() def carboncarbon(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('asp1', 'name od1 within %s of name nz'%(self.range.get()*3.5)) cmd.select('asp2', 'resn asp within %s of name ne2'%(self.range.get()*6)) cmd.select('asp', 'byres asp1 and byres asp2') cmd.select('lys1', 'name nz within %s of asp'%(self.range.get()*6)) cmd.select('lys2', 'resn lys within %s of resn his'%(self.range.get()*8)) cmd.select('lys', 'byres lys1 and byres lys2') cmd.select('his1', 'name ne2 within %s of name nz'%(self.range.get()*6)) cmd.select('his2', 'resn his within %s of lys'%(self.range.get()*6)) cmd.select('his3', 'resn his within %s of asp'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3') cmd.select('carboncarbon', 'asp(lys(his))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'carboncarbon') cmd.delete('his1') cmd.delete('lys1') cmd.delete('glu1') cmd.orient('carboncarbon') self.cpkcarboncarbon() cmd.deselect() cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his') def peroxidase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('asn1', 'name od1 within %s of name nd1'%(self.range.get()*8)) cmd.select('asn2', 'name od1 within %s of name ne2'%(self.range.get()*6)) cmd.select('asn3', 'name nd2 within %s of name nd1'%(self.range.get()*10)) cmd.select('asn4', 'name nd2 within %s of name ne2'%(self.range.get()*8)) cmd.select('asn5', 'name od1 within %s of name nh2'%(self.range.get()*7)) cmd.select('asn6', 'name od1 within %s of name nh1'%(self.range.get()*8.6))#measure more cmd.select('asn7', 'name od1 within %s of name ne'%(self.range.get()*8)) cmd.select('asn8', 'name nd2 within %s of name nh2'%(self.range.get()*9)) cmd.select('asn9', 'name nd2 within %s of name nh1'%(self.range.get()*11))# cmd.select('asn10', 'name nd2 within %s of name ne'%(self.range.get()*9.8)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10') cmd.select('his1', 'name nd1 within %s of name od1'%(self.range.get()*5)) cmd.select('his2','name ne2 within %s of name od1'%(self.range.get()*5)) cmd.select('his3', 'name nd1 within %s of name nd2'%(self.range.get()*8))# cmd.select('his4', 'name ne2 within %s of name nd2'%(self.range.get()*8.5))# cmd.select('his5', 'name ne2 within %s of name ne'%(self.range.get()*5.8)) cmd.select('his6', 'name ne2 within %s of name nh2'%(self.range.get()*6))# cmd.select('his7', 'name ne2 within %s of name nh1'%(self.range.get()*8.2))# cmd.select('his8', 'name nd1 within %s of name nh1'%(self.range.get()*7.2))# cmd.select('his9', 'name nd1 within %s of name nh2'%(self.range.get()*5.8)) cmd.select('his10', 'name nd1 within %s of name ne'%(self.range.get()*7)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('arg1', 'name nh2 within %s of name od1'%(self.range.get()*7.5)) cmd.select('arg2', 'name nh2 within %s of name nd2'%(self.range.get()*9.5)) cmd.select('arg3', 'name nh2 within %s of name ne2'%(self.range.get()*6))# cmd.select('arg4', 'name nh2 within %s of name nd1'%(self.range.get()*6)) cmd.select('arg5', 'name nh1 within %s of name od1'%(self.range.get()*8))# cmd.select('arg6', 'name nh1 within %s of name nd2'%(self.range.get()*10)) cmd.select('arg7', 'name nh1 within %s of name ne2'%(self.range.get()*8))# cmd.select('arg8', 'name nh1 within %s of name nd1'%(self.range.get()*7.4))# cmd.select('arg9', 'name ne within %s of name od1'%(self.range.get()*7.2)) cmd.select('arg10', 'name ne within %s of name nd2'%(self.range.get()*8.9)) cmd.select('arg11', 'name ne within %s of name ne2'%(self.range.get()*5.9)) cmd.select('arg12', 'name ne within %s of name nd1'%(self.range.get()*6)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byres arg11 and byres arg12') cmd.select('Peroxidase', 'asn(his(arg))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Peroxidase') self.cpkperoxidase() cmd.orient('Peroxidase') cmd.deselect() cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg12') cmd.delete('arg') def trioseisomerase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('lys1', 'name nz and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('lys2', 'name nz and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('lys4', 'name ce and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys5', 'name ce and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys6', 'name ce and resn lys within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('lys7', 'name cd and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*6.2)) cmd.select('lys8', 'name cd and resn lys within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('lys9', 'name cd and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys10', 'name nz and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('lys11', 'name nz and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7.5)) cmd.select('lys12', 'name nz and resn lys within %s of (name ce1 and resn his)'%(self.range.get()*6.7)) cmd.select('lys13', 'name nz and resn lys within %s of (name cd2 and resn his)'%(self.range.get()*7.5)) cmd.select('lys14', 'name nz and resn lys within %s of (name cg and resn his)'%(self.range.get()*8)) cmd.select('lys15', 'name ce and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*6.2)) cmd.select('lys16', 'name ce and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7.6)) cmd.select('lys17', 'name ce and resn lys within %s of (name ce1 and resn his)'%(self.range.get()*6.6)) cmd.select('lys18', 'name ce and resn lys within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('lys19', 'name ce and resn lys within %s of (name cg and resn his)'%(self.range.get()*7.5)) cmd.select('lys20', 'name nz and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*8.5)) cmd.select('lys21', 'name nz and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*10)) cmd.select('lys22', 'name nz and resn lys within %s of (name cd and resn glu)'%(self.range.get()*9.5)) cmd.select('lys23', 'name ce and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*9)) cmd.select('lys24', 'name ce and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*10.2)) cmd.select('lys25', 'name ce and resn lys within %s of (name cd and resn glu)'%(self.range.get()*10)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13 and byres lys14 and byres lys15 and byres lys16 and byres lys17 and byres lys18 and byres lys19 and byres lys20 and byres lys21 and byres lys22 and byres lys23 and byres lys24 and byres lys25') cmd.select('asn1', 'name od1 and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn2', 'name nd2 and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn3', 'name cg and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn6', 'name cg and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn7', 'name od1 and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.2)) cmd.select('asn8', 'name cg and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.5)) cmd.select('asn10', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*6.3)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*6.2)) cmd.select('asn12', 'name nd2 and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*7.3)) cmd.select('asn13', 'name nd2 and resn asn within %s of (name nd1 and resn his)'%(self.range.get()*8)) cmd.select('asn14', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn15', 'name od1 and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*9.2)) cmd.select('asn16', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*8.3)) cmd.select('asn17', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7.5)) cmd.select('asn18', 'name cg and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*8.5)) cmd.select('asn19', 'name cg and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7.5)) cmd.select('asn20', 'name nd2 and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*9)) cmd.select('asn21', 'name nd2 and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*10.5)) cmd.select('asn22', 'name nd2 and resn asn within %s of (name cd and resn glu)'%(self.range.get()*10.2)) cmd.select('asn23', 'name cg and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*10)) cmd.select('asn24', 'name cg and resn asn within %s of (name cd and resn glu)'%(self.range.get()*11)) cmd.select('asn25', 'name cg and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*11.3)) cmd.select('asn26', 'name od1 and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*11)) cmd.select('asn27', 'name od1 and resn asn within %s of (name cd and resn glu)'%(self.range.get()*11)) cmd.select('asn28', 'name od1 and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*12)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11 and byres asn12 and byres asn13 and byres asn14 and byres asn15 and byres asn16 and byres asn17 and byres asn18 and byres asn19 and byres asn20 and byres asn21 and byres asn22 and byres asn23 and byres asn24 and byres asn25 and byres asn26 and byres asn27 and byres asn28') cmd.select('glu1', 'name oe2 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*8.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*10)) cmd.select('glu3', 'name cd and resn glu within %s of (name nz and resn lys)'%(self.range.get()*9.5)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*9)) cmd.select('glu5', 'name oe1 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*10.2)) cmd.select('glu6', 'name cd and resn glu within %s of (name ce and resn lys)'%(self.range.get()*10)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*9)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*10.5)) cmd.select('glu9', 'name cd and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*10.2)) cmd.select('glu10', 'name oe2 and resn glu within %s of (name cg and resn asn)'%(self.range.get()*10)) cmd.select('glu11', 'name cd and resn glu within %s of (name cg and resn asn)'%(self.range.get()*11)) cmd.select('glu12', 'name oe1 and resn glu within %s of (name cg and resn asn)'%(self.range.get()*11.3)) cmd.select('glu13', 'name oe2 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('glu14', 'name cd and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('glu15', 'name oe1 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*12)) cmd.select('glu16', 'name oe2 and resn glu within %s of (name ne2 and resn his)'%(self.range.get()*5.6)) cmd.select('glu17', 'name oe2 and resn glu within %s of (name cd2 and resn his)'%(self.range.get()*6.5)) cmd.select('glu18', 'name oe2 and resn glu within %s of (name ce1 and resn his)'%(self.range.get()*5.8)) cmd.select('glu19', 'name oe2 and resn glu within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('glu20', 'name oe2 and resn glu within %s of (name cg and resn his)'%(self.range.get()*6.6)) cmd.select('glu21', 'name oe1 and resn glu within %s of (name ne2 and resn his)'%(self.range.get()*6.6)) cmd.select('glu22', 'name oe1 and resn glu within %s of (name cd2 and resn his)'%(self.range.get()*6.5)) cmd.select('glu23', 'name oe1 and resn glu within %s of (name ce1 and resn his)'%(self.range.get()*5.8)) cmd.select('glu24', 'name oe1 and resn glu within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('glu25', 'name oe1 and resn glu within %s of (name cg and resn his)'%(self.range.get()*6.6)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11 and byres glu12 and byres glu13 and byres glu14 and byres glu15 and byres glu16 and byres glu17 and byres glu18 and byres glu19 and byres glu20 and byres glu21 and byres glu22 and byres glu23 and byres glu24 and byres glu25') cmd.select('his1', 'name ne2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*6.5)) cmd.select('his2', 'name nd1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his3', 'name ce1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*6.7)) cmd.select('his4', 'name cd2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his5', 'name cg and resn his within %s of (name nz and resn lys)'%(self.range.get()*8)) cmd.select('his6', 'name ne2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*6.2)) cmd.select('his7', 'name nd1 and resn his within %s of (name ce and resn lys)'%(self.range.get()*7.6)) cmd.select('his8', 'name ce1 and resn his within %s of (name ce and resn lys)'%(self.range.get()*6.6)) cmd.select('his9', 'name cd2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*7)) cmd.select('his10', 'name cg and resn his within %s of (name ce and resn lys)'%(self.range.get()*7.5)) cmd.select('his11', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*6.3)) cmd.select('his12', 'name cd2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*6.2)) cmd.select('his13', 'name ce1 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*7.3)) cmd.select('his14', 'name nd1 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his15', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*8)) cmd.select('his16', 'name ce1 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*9.2)) cmd.select('his17', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*8.3)) cmd.select('his18', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('his19', 'name ce1 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8.5)) cmd.select('his20', 'name cd2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('his21', 'name ne2 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*5.6)) cmd.select('his22', 'name cd2 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('his23', 'name ce1 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*5.8)) cmd.select('his24', 'name nd1 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('his25', 'name cg and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.6)) cmd.select('his26', 'name ne2 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.6)) cmd.select('his27', 'name cd2 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('his28', 'name ce1 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*5.8)) cmd.select('his29', 'name nd1 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('his30', 'name cg and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.6)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13 and byres his14 and byres his15 and byres his16 and byres his17 and byres his18 and byres his19 and byres his20 and byres his21 and byres his22 and byres his23 and byres his24 and byres his25 and byres his26 and byres his27 and byres his28 and byres his29 and byres his30') cmd.select('TrioseIsomerase', 'glu(his(asn(lys)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'TrioseIsomerase') self.cpktriose() cmd.orient('TrioseIsomerase') cmd.deselect() cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn12') cmd.delete('asn13') cmd.delete('asn14') cmd.delete('asn15') cmd.delete('asn16') cmd.delete('asn17') cmd.delete('asn18') cmd.delete('asn19') cmd.delete('asn20') cmd.delete('asn21') cmd.delete('asn22') cmd.delete('asn23') cmd.delete('asn24') cmd.delete('asn25') cmd.delete('asn26') cmd.delete('asn27') cmd.delete('asn28') cmd.delete('asn') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his14') cmd.delete('his15') cmd.delete('his16') cmd.delete('his17') cmd.delete('his18') cmd.delete('his19') cmd.delete('his20') cmd.delete('his21') cmd.delete('his22') cmd.delete('his23') cmd.delete('his24') cmd.delete('his25') cmd.delete('his26') cmd.delete('his27') cmd.delete('his28') cmd.delete('his29') cmd.delete('his30') cmd.delete('his') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu12') cmd.delete('glu13') cmd.delete('glu14') cmd.delete('glu15') cmd.delete('glu16') cmd.delete('glu17') cmd.delete('glu18') cmd.delete('glu19') cmd.delete('glu20') cmd.delete('glu21') cmd.delete('glu22') cmd.delete('glu23') cmd.delete('glu24') cmd.delete('glu25') cmd.delete('glu') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys14') cmd.delete('lys15') cmd.delete('lys16') cmd.delete('lys17') cmd.delete('lys18') cmd.delete('lys19') cmd.delete('lys20') cmd.delete('lys21') cmd.delete('lys22') cmd.delete('lys23') cmd.delete('lys24') cmd.delete('lys25') cmd.delete('lys') def alcoholdehyd(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('tyr1', 'name cd1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*5)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*8)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name nz and resn lys)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('tyr5', 'name ce2 and resn tyr within %s of (name cg and resn lys)'%(self.range.get()*6)) cmd.select('tyr6', 'name cg and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7') cmd.select('asn1', 'name nd2 and resn asn within %s of (name cd1 and tyr)'%(self.range.get()*5)) cmd.select('asn2', 'name nd2 and resn asn within %s of (name oh and tyr)'%(self.range.get()*7)) cmd.select('asn3', 'name od1 and resn asn within %s of (name oh and tyr)'%(self.range.get()*7)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ce1 and tyr)'%(self.range.get()*6)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*5.5)) cmd.select('asn6', 'name od1 and resn asn within %s5 of (name nz and resn lys)'%(self.range.get()*5.5)) cmd.select('asn7', 'name nd2 and resn asn within %s of (name og and resn ser)'%(self.range.get()*10)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7') cmd.select('lys1', 'name nz and resn lys within %s of (name od1 and asn)'%(self.range.get()*6)) cmd.select('lys2', 'name ce and resn lys within %s of (name nd2 and asn)'%(self.range.get()*6.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('lys4', 'name ce and resn lys within %s of (name cz and tyr)'%(self.range.get()*6)) cmd.select('lys4', 'name nz and resn lys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('lys5', 'name ce and resn lys within %s of (name og and resn ser)'%(self.range.get()*7)) cmd.select('lys6', 'name cg and resn lys within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('lys7', 'name cd and resn lys within %s of (name cb and resn ser)'%(self.range.get()*6)) cmd.select('lys8', 'name cd and resn lys within %s of (name cb and resn asn)'%(self.range.get()*7)) cmd.select('lys9', 'name ce and resn lys within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9') cmd.select('ser1', 'name og and resn ser within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('ser2', 'name og and resn ser within %s of (name ce2 and tyr)'%(self.range.get()*6)) cmd.select('ser3', 'name og and resn ser within %s of (name nz and lys)'%(self.range.get()*8)) cmd.select('ser4', 'name cb and resn ser within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('ser5', 'name cb and resn ser within %s of (name cd and lys)'%(self.range.get()*6)) cmd.select('ser6', 'name cb and resn ser within %s of (name od1 and asn)'%(self.range.get()*10)) cmd.select('ser7', 'name ca and resn ser within %s of (name nd2 and asn)'%(self.range.get()*10)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7') cmd.select('alcoholdehyd','ser(tyr(lys(asn)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'alcoholdehyd') self.cpkalcoholdehyd() cmd.orient('alcoholdehyd') cmd.deselect() cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('asn') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('lys') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys1') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') def aldoreductase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('lys1', 'name cd and resn lys within %s of (name cg and resn his)'%(self.range.get()*6)) cmd.select('lys2', 'name ce and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('lys3', 'name cd and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('lys4', 'name nz and resn lys within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('lys5', 'name nz and resn lys within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('lys6', 'name cg and resn lys within %s of (name cz and resn tyr)'%(self.range.get()*8)) cmd.select('lys7', 'name nz and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('lys8', 'name ce and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*5.5)) cmd.select('lys9', 'name cg and resn lys within %s of (name ca and resn asp)'%(self.range.get()*9)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9') cmd.select('his1', 'name cg and resn his within %s of (name cd and resn lys)'%(self.range.get()*6)) cmd.select('his2', 'name ne2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*8)) cmd.select('his3', 'name nd1 and resn his within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his5', 'name ce1 and resn his within %s of (name cz and resn tyr)'%(self.range.get()*6)) cmd.select('his6', 'name nd1 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*10.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name cg and resn asp)'%(self.range.get()*10)) cmd.select('his9', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('tyr1', 'name oh and resn tyr within %s of (name nz and resn lys )'%(self.range.get()*5)) cmd.select('tyr2', 'name ce2 and resn tyr within %s of (name nz and resn lys )'%(self.range.get()*6)) cmd.select('tyr3', 'name cz and resn tyr within %s of (name cg and resn lys)'%(self.range.get()*8)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr5', 'name cz and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*6)) cmd.select('tyr6', 'name ce1 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('tyr8', 'name cz and resn tyr within %s of (name cb and resn asp)'%(self.range.get()*9)) cmd.select('tyr9', 'name ce2 and resn tyr within %s of (name ca and resn asp)'%(self.range.get()*8)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9') cmd.select('asp1', 'name od1 and resn asp within %s of (name nz and resn lys)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name ce and resn lys)'%(self.range.get()*5.5)) cmd.select('asp3', 'name ca and resn asp within %s of (name cg and resn lys)'%(self.range.get()*9)) cmd.select('asp4', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*10.5)) cmd.select('asp5', 'name cg and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*10)) cmd.select('asp6', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*9)) cmd.select('asp7', 'name od2 and resn asp within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('asp8', 'name cb and resn asp within %s of (name cz and resn tyr)'%(self.range.get()*9)) cmd.select('asp9', 'name ca and resn asp within %s of (name ce2 and resn tyr)'%(self.range.get()*8)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('aldoreductase', 'asp(his(lys(tyr)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'aldoreductase') cmd.orient('aldoreductase') self.cpkaldoreductase() cmd.deselect() cmd.delete('lys') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys1') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') def cistransisomerase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*9)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name od1 and resn asp)'%(self.range.get()*11)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cg and resn asp)'%(self.range.get()*9.8)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name cb and resn asp)'%(self.range.get()*9.8)) cmd.select('tyr5', 'name cz and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*10.2)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name od1 and resn asp)'%(self.range.get()*11.5)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr8', 'name oh and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr9', 'name oh and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr10', 'name cz and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr11', 'name cz and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.8)) cmd.select('tyr12', 'name cz and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.3)) cmd.select('tyr14', 'name ce1 and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr15', 'name ce1 and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr', 'byres tyr1 and byre tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13 and byres tyr14 and byres tyr15') cmd.select('asp1', 'name od2 and resn asp within %s of (name oh and tyr)'%(self.range.get()*8.7)) cmd.select('asp2', 'name od1 and resn asp within %s of (name oh and tyr)'%(self.range.get()*10.5)) cmd.select('asp3', 'name cg and resn asp within %s of (name oh and tyr)'%(self.range.get()*9.3)) cmd.select('asp4', 'name cb and resn asp within %s of (name oh and tyr)'%(self.range.get()*9.3)) cmd.select('asp5', 'name od2 and resn asp within %s of (name cz and tyr)'%(self.range.get()*10)) cmd.select('asp6', 'name od1 and resn asp within %s of (name cz and resn tyr)'%(self.range.get()*11.1)) cmd.select('asp7', 'name od2 and resn asp within %s of (name cg2 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cd1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp9', 'name od2 and resn asp within %s of (name cg1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp10', 'name cb and resn asp within %s of (name cd1 and resn ile)'%(self.range.get()*10.8)) cmd.select('asp11', 'name cb and resn asp within %s of (name cg2 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp12', 'name cb and resn asp within %s of (name cg1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10 and byres asp11 and byres asp12') cmd.select('ile1', 'name cd1 and resn ile within %s of (name oh and tyr)'%(self.range.get()*6.5)) cmd.select('ile2', 'name cg1 and resn ile within %s of (name oh and tyr)'%(self.range.get()*6.5)) cmd.select('ile3', 'name cg2 and resn ile within %s of (name oh and tyr)'%(self.range.get()*5.5)) cmd.select('ile4', 'name cd1 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*6.5)) cmd.select('ile5', 'name cg1 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*6.8)) cmd.select('ile6', 'name cg2 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*5.5)) cmd.select('ile7', 'name cd1 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*6.3)) cmd.select('ile8', 'name cg1 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('ile9', 'name cg2 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*5.5)) cmd.select('ile10', 'name cg2 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile11', 'name cd1 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile12', 'name cg1 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile13', 'name cd1 and resn ile within %s of (name cb and asp)'%(self.range.get()*11)) cmd.select('ile14', 'name cg2 and resn ile within %s of (name cb and resn asp)'%(self.range.get()*11.5)) cmd.select('ile15', 'name cg1 and resn ile within %s of (name cb and resn asp)'%(self.range.get()*11.5)) cmd.select('ile', 'byres ile1 and byres ile2 and byres ile3 and byres ile4 and byres ile5 and byres ile6 and byres ile7 and byres ile8 and byres ile9 and byres ile10 and byres ile11 and byres ile12 and byres ile13 and byres ile14 and byres ile15') cmd.select('Cis-trans', 'ile(asp(tyr))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Cis-trans') self.cpkcistrans() cmd.deselect() cmd.orient('Cis-trans') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr2') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('tyr14') cmd.delete('tyr15') cmd.delete('tyr') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp11') cmd.delete('asp12') cmd.delete('asp') cmd.delete('ile1') cmd.delete('ile2') cmd.delete('ile3') cmd.delete('ile4') cmd.delete('ile5') cmd.delete('ile6') cmd.delete('ile7') cmd.delete('ile8') cmd.delete('ile9') cmd.delete('ile10') cmd.delete('ile11') cmd.delete('ile12') cmd.delete('ile13') cmd.delete('ile14') cmd.delete('ile15') cmd.delete('ile') def nadhbinder(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('asp1', 'name od2 and resn asp within %s of (name sg and resn cys)'%(self.range.get()*5)) cmd.select('asp2', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name sg and resn cys)'%(self.range.get()*6.4)) cmd.select('asp4', 'name od1 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*7.2)) cmd.select('asp5', 'name cg and resn asp within %s of (name sg and resn cys)'%(self.range.get()*5.5)) cmd.select('asp6', 'name od2 and resn asp within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('asp7', 'name od2 and resn asp within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('asp8', 'name od1 and resn asp within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('asp9', 'name od1 and resn asp within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('asp10', 'name cg and resn asp within %s of (name og and resn ser)'%(self.range.get()*5.3)) cmd.select('asp11', 'name cg and resn asp within %s of (name cb and resn ser)'%(self.range.get()*6.4)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10 and byres asp11') cmd.select('cys1', 'name sg and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*5)) cmd.select('cys2', 'name cb and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('cys3', 'name sg and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*6.4)) cmd.select('cys4', 'name cb and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*7.2)) cmd.select('cys5', 'name sg and resn cys within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('cys6', 'name sg and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.4)) cmd.select('cys7', 'name sg and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name og and resn ser)'%(self.range.get()*8)) cmd.select('cys9', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*8.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('ser4', 'name cb and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('ser5', 'name og and resn ser within %s of (name cg and resn asp)'%(self.range.get()*5.3)) cmd.select('ser6', 'name cb and resn ser within %s of (name cg and resn asp)'%(self.range.get()*6.4)) cmd.select('ser7', 'name og and resn ser within %s of (name sg and resn cys)'%(self.range.get()*6.4)) cmd.select('ser8', 'name cb and resn ser within %s of (name sg and resn cys)'%(self.range.get()*7)) cmd.select('ser9', 'name og and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8)) cmd.select('ser10', 'name cb and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10') cmd.select('NAD-reductase', 'ser(asp(cys))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'NAD-reductase') self.cpknadreductase() cmd.deselect() cmd.orient('NAD-reductase') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp11') cmd.delete('asp') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.delete('cys') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser') def nadhbinder2(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('glu2', 'name oe2 and resn glu within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('glu4', 'name oe1 and resn glu within %s of (name cb and resn cys)'%(self.range.get()*7.2)) cmd.select('glu5', 'name cg and resn glu within %s of (name sg and resn cys)'%(self.range.get()*5.5)) cmd.select('glu6', 'name oe2 and resn glu within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('glu9', 'name oe1 and resn glu within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('glu10', 'name cg and resn glu within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('glu11', 'name cg and resn glu within %s of (name cb and resn ser)'%(self.range.get()*6.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11') cmd.select('cys1', 'name sg and resn cys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys3', 'name sg and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys4', 'name cb and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*7.5)) cmd.select('cys5', 'name sg and resn cys within %s of (name cg and resn glu)'%(self.range.get()*5.5)) cmd.select('cys6', 'name sg and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.5)) cmd.select('cys7', 'name sg and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name og and resn ser)'%(self.range.get()*8)) cmd.select('cys9', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*8.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name oe2 and resn glu)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name oe2 and resn glu)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name oe1 and resn glu)'%(self.range.get()*6)) cmd.select('ser4', 'name cb and resn ser within %s of (name oe1 and resn glu)'%(self.range.get()*7)) cmd.select('ser5', 'name og and resn ser within %s of (name cg and resn glu)'%(self.range.get()*5.5)) cmd.select('ser6', 'name cb and resn ser within %s of (name cg and resn glu)'%(self.range.get()*6.5)) cmd.select('ser7', 'name og and resn ser within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('ser8', 'name cb and resn ser within %s of (name sg and resn cys)'%(self.range.get()*7)) cmd.select('ser9', 'name og and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8)) cmd.select('ser10', 'name cb and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10') cmd.select('NAD-reductase2', 'ser(glu(cys))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'NAD-reductase2') self.cpknadreductase2() cmd.deselect() cmd.orient('NAD-reductase2') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.delete('cys') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser') def cephdeacetylase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*4.5)) cmd.select('his2', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('his3', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('his4', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his5', 'name ce1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('his6', 'name ne2 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('his7', 'name ne2 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*6.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('his9', 'name ce1 and resn his within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('his10', 'name nd1 and resn his within %s of (name cb and resn ala)'%(self.range.get()*6.5)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('asp1', 'name od2 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8.5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9.5)) cmd.select('asp3', 'name cg and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9.5)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*4.5)) cmd.select('asp5', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5)) cmd.select('asp6', 'name cg and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp7', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp8', 'name od1 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*6)) cmd.select('asp9', 'name od1 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asp10', 'name od2 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10') cmd.select('ala1', 'name cb and resn ala within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('ala2', 'name cb and resn ala within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('ala3', 'name cb and resn ala within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('ala4', 'name cb and resn ala within %s of (name od2 and resn asp)'%(self.range.get()*8.5)) cmd.select('ala5', 'name cb and resn ala within %s of (name od1 and resn asp)'%(self.range.get()*9.5)) cmd.select('ala6', 'name cb and resn ala within %s of (name cg and resn asp)'%(self.range.get()*9.5)) cmd.select('ala7', 'name c and resn ala within %s of (name n and resn gln)'%(self.range.get()*2.5)) cmd.select('ala', 'byres ala1 and byres ala2 and byres ala3 and byres ala4 and byres ala5 and byres ala6 and byres ala7') cmd.select('gln1', 'byres resn gln within %s of his'%(self.range.get()*9.5)) cmd.select('gln2', 'byres resn gln within %s of asp'%(self.range.get()*13.5)) cmd.select('gln3', 'byres resn gln within %s of ala'%(self.range.get()*3)) cmd.select('gln', 'byres gln1 and byres gln2 and byres gln3') cmd.select('deacetylase', 'his(asp(ala(gln)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'deacetylase') self.cpkdeacetylase() cmd.deselect() cmd.orient('deacetylase') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp') cmd.delete('ala1') cmd.delete('ala2') cmd.delete('ala3') cmd.delete('ala4') cmd.delete('ala5') cmd.delete('ala6') cmd.delete('ala7') cmd.delete('ala') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln') #hyaluronate/chondroitin lyase def chondrolyase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name nh2 and resn arg)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne and resn arg)'%(self.range.get()*7)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*5)) cmd.select('tyr6', 'name oh and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*5)) cmd.select('tyr8', 'name ce2 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr9', 'name ce1 and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr12', 'name ce1 and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13') cmd.select('his1', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his2', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his3', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8)) cmd.select('his5', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his6', 'name nd1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his7', 'name ce1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('his9', 'name ne2 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('his10', 'name ne2 and resn his within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('his11', 'name ce1 and resn his within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('his12', 'name nd1 and resn his within %s of (name nh1 and resn arg)'%(self.range.get()*6.5)) cmd.select('his13', 'name nd1 and resn his within %s of (name cd and resn arg)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13') cmd.select('arg1', 'name nh2 and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg2', 'name nh1 and resn arg within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('arg3', 'name cz and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg4', 'name ne and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('arg6', 'name cz and resn arg within %s of (name ce1 and resn his)'%(self.range.get()*7)) cmd.select('arg7', 'name nh1 and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('arg8', 'name cd and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*9)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('arg10', 'name cz and resn arg within %s of (name cg and resn asn)'%(self.range.get()*12)) cmd.select('arg11', 'name nh2 and resn arg within %s of (name nd2 and resn asn)'%(self.range.get()*11.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byre arg11') cmd.select('asn1', 'name od1 and resn asn within %s of (name nh1 and resn arg)'%(self.range.get()*11)) cmd.select('asn2', 'name cg and resn asn within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('asn3', 'name nd2 and resn asn within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn6', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asn7', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn8', 'name od1 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn10', 'name od1 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11') cmd.select('chondroitinase', 'asn(his(arg(tyr)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'chondroitinase') cmd.deselect() self.cpkchondro() cmd.orient('chondroitinase') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg') def hyaluronlyase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name nh2 and resn arg)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne and resn arg)'%(self.range.get()*7)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*5)) cmd.select('tyr6', 'name oh and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*5)) cmd.select('tyr8', 'name ce2 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr9', 'name ce1 and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr12', 'name ce1 and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13') cmd.select('his1', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his2', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his3', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8)) cmd.select('his5', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his6', 'name nd1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his7', 'name ce1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('his9', 'name ne2 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('his10', 'name ne2 and resn his within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('his11', 'name ce1 and resn his within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('his12', 'name nd1 and resn his within %s of (name nh1 and resn arg)'%(self.range.get()*6.5)) cmd.select('his13', 'name nd1 and resn his within %s of (name cd and resn arg)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13') cmd.select('arg1', 'name nh2 and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg2', 'name nh1 and resn arg within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('arg3', 'name cz and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg4', 'name ne and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('arg6', 'name cz and resn arg within %s of (name ce1 and resn his)'%(self.range.get()*7)) cmd.select('arg7', 'name nh1 and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('arg8', 'name cd and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*9)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('arg10', 'name cz and resn arg within %s of (name cg and resn asn)'%(self.range.get()*12)) cmd.select('arg11', 'name nh2 and resn arg within %s of (name nd2 and resn asn)'%(self.range.get()*11.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byre arg11') cmd.select('asn1', 'name od1 and resn asn within %s of (name nh1 and resn arg)'%(self.range.get()*11)) cmd.select('asn2', 'name cg and resn asn within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('asn3', 'name nd2 and resn asn within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn6', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asn7', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn8', 'name od1 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn10', 'name od1 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11') cmd.select('Hyaluronate_Lyase', 'asn(his(arg(tyr)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Hyaluronate_Lyase') cmd.deselect() self.cpkhyaluron() cmd.orient('Hyaluronate_Lyase') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg') def ACTase(self): import tkMessageBox tkMessageBox.showinfo('Info', 'This motif is based on sequence not position') self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('gln', 'resi 231 and resn gln') cmd.select('arg', 'resi 167 and resn arg(resi 229 and resn arg)') cmd.select('thr', 'resi 55 and resn thr(resi 53 and resn thr)') cmd.select('his', 'resi 134 and resn his') cmd.select('lys', 'resi 84 and resn lys') cmd.select('ser', 'resi 80 and resn ser') cmd.select('actase', 'gln(arg(thr(his(lys(ser)))))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'actase') self.cpkactase() cmd.deselect() cmd.orient('actase') cmd.delete('arg') cmd.delete('lys') cmd.delete('thr') cmd.delete('ser') cmd.delete('gln') cmd.delete('his') def ACTase2(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('gln', 'resi 231 and resn gln') cmd.select('arg', 'resi 167 and resn arg(resi 229 and resn arg)') cmd.select('thr', 'resi 55 and resn thr(resi 53 and resn thr)') cmd.select('his', 'resi 134 and resn his') cmd.select('lys', 'resi 84 and resn lys') cmd.select('ser', 'resi 80 and resn ser') cmd.select('actase', 'gln(arg(thr(his(lys(ser)))))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'actase') self.cpkactase() cmd.deselect() cmd.orient('actase') cmd.delete('arg') cmd.delete('lys') cmd.delete('thr') cmd.delete('ser') cmd.delete('gln') cmd.delete('his') def exonucleaseiii(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*5.5)) cmd.select('his2', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('his3', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*5.5)) cmd.select('his4', 'name cd2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*5.5)) cmd.select('his5', 'name nd1 and resn his within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('his6', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his7', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5.5)) cmd.select('his9', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('asp1', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp4', 'name cg and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp5', 'name od2 and resn asp within %s of (name nd2 and resn asn)'%(self.range.get()*5.7)) cmd.select('asp6', 'name od1 and resn asp within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('asp7', 'name od1 and resn asp within %s of (name od1 and resn asn)'%(self.range.get()*6)) cmd.select('asp8', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7') cmd.select('asp9', 'byres resn asp within %s of asp8'%(self.range.get()*5.5)) cmd.select('asp10', 'byres resn asp within %s of his'%(self.range.get()*5.5)) cmd.select('asp', 'byres asp8 or (byres asp9 and byres asp10)') cmd.select('asn1', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn2', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('asn3', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn4', 'name cg and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn5', 'name cg and resn asn within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('asn6', 'name nd2 and resn asn within %s of (name od2 and resn asp)'%(self.range.get()*5.7)) cmd.select('asn7', 'name nd2 and resn asn within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('asn8', 'name od1 and resn asn within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('asn9', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8') cmd.select('asn10', 'byres resn asn within %s of asn9'%(self.range.get()*8)) cmd.select('asn11', 'byres resn asn within %s of his'%(self.range.get()*8)) cmd.select('asn12', 'byres resn asn within %s of asp8'%(self.range.get()*6)) cmd.select('asn', 'byres asn9 or (byres asn10 and byres asn11 and byres asn12)') cmd.select('Exonuclease3', 'his(asp(asn))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Exonuclease3') self.cpknuclease() cmd.orient('Exonuclease3') cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn12') cmd.delete('asn') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp') def cyclinkinase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*6.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('glu3', 'name cd and resn glu within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('glu4', 'name oe1 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu5', 'name cd and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu6', 'name oe1 and resn glu within %s of (name cd and resn lys)'%(self.range.get()*5.5)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name cg and resn lys)'%(self.range.get()*5.5)) cmd.select('glu9', 'name oe1 and resn glu within %s of (name od1 and resn asp)'%(self.range.get()*10)) cmd.select('glu10', 'name oe2 and resn glu within %s of (name od1 and resn asp)'%(self.range.get()*10)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10') cmd.select('lys1', 'name nz and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('lys2', 'name nz and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*7)) cmd.select('lys3', 'name nz and resn lys within %s of (name cd and glu)'%(self.range.get()*7)) cmd.select('lys4', 'name ce and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*6)) cmd.select('lys5', 'name ce and resn lys within %s of (name cd and resn glu)'%(self.range.get()*6)) cmd.select('lys6', 'name cd and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*5.5)) cmd.select('lys7', 'name ce and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*6)) cmd.select('lys8', 'name cg and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*5.5)) cmd.select('lys9', 'name nz and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys10', 'name nz and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*6)) cmd.select('lys11', 'name ce and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys12', 'name ce and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*6.5)) cmd.select('lys13', 'name cd and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys14', 'name cd and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13 and byres lys14') cmd.select('asp1', 'name od1 and resn asp within %s of (name oe1 and glu)'%(self.range.get()*10)) cmd.select('asp2', 'name od1 and resn asp within %s of (name oe2 and glu)'%(self.range.get()*10)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nz and lys)'%(self.range.get()*6)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nz and lys)'%(self.range.get()*6)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ce and lys)'%(self.range.get()*6)) cmd.select('asp6', 'name od2 and resn asp within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name cd and resn lys)'%(self.range.get()*6)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('asp9', 'name cg and resn asp within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('Cyclin_Kinase', 'lys(asp(glu))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Cyclin_Kinase') self.cpkcyclinkinase() cmd.orient('Cyclin_Kinase') cmd.deselect() cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys14') cmd.delete('lys') def adenylatekinase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() #p-loop first cmd.select('lys1', 'name nz and resn lys within %s of (name n and resn gly)'%(self.range.get()*7.5)) cmd.select('lys2', 'name cg and resn lys within %s of (name c and resn gly)'%(self.range.get()*6)) cmd.select('lys3', 'name n and resn lys within %s of (name n and resn gly)'%(self.range.get()*5)) cmd.select('lys4', 'name n and resn lys within %s of (resn gly)'%(self.range.get()*2)) cmd.select('lys5', 'name c and resn lys within %s of (resn gly)'%(self.range.get()*2)) cmd.select('lys6', 'name nz and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*13)) cmd.select('lys7', 'name nz and resn lys within %s of (name ne and resn arg)'%(self.range.get()*11)) cmd.select('lys8', 'name nz and resn lys within %s of (name nh2 and resn arg)'%(self.range.get()*9.5)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8') cmd.select('glya1', 'name n and resn gly within %s of (name nz and lys)'%(self.range.get()*7.5)) cmd.select('glya2', 'name ca and resn gly within %s of (name cg and lys)'%(self.range.get()*7)) cmd.select('glya3', 'name c and resn gly within %s of (name n and lys)'%(self.range.get()*2)) cmd.select('glya4', 'name n and resn gly within %s of (name nh1 and resn arg)'%(self.range.get()*10)) cmd.select('glya', 'byres glya1 and byres glya2 and byres glya3 and byres glya4') cmd.select('glyb', 'name n and resn gly within %s of (name c and lys)'%(self.range.get()*2)) cmd.select('p-loop', 'lys(glya(byres glyb))') cmd.select('asp1', 'name od2 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('asp4', 'name od2 and resn asp within %s of p-loop'%(self.range.get()*15)) cmd.select('aspa', 'byres asp1 and byres asp2 and byres asp3 and byres asp4') cmd.select('aspb1', 'name od2 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('aspb2', 'name cg and resn asp within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('aspb3', 'name od1 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('aspb4', 'name od2 and resn asp within %s of (name od1 and aspa)'%(self.range.get()*7)) cmd.select('aspb5', 'name cg and resn asp within %s of (name cg and aspa)'%(self.range.get()*7)) cmd.select('aspb6', 'name od1 and resn asp within %s of (name od2 and aspa)'%(self.range.get()*7)) cmd.select('asp', 'byres aspb1 and byres aspb2 and byres aspb3 and byres aspb4 and byres aspb5 and byres aspb6') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and asp or name od2 and asp)'%(self.range.get()*4.9)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od1 and asp or name od2 and asp)'%(self.range.get()*4.9)) cmd.select('arg', 'byres arg1 or byres arg2') cmd.select('adenylatekinase', 'p-loop(asp(aspa(arg)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'adenylatekinase') self.cpkadenylatekinase() cmd.deselect() cmd.orient('adenylatekinase') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys') cmd.delete('glya1') cmd.delete('glya2') cmd.delete('glya3') cmd.delete('glya4') cmd.delete('glya') cmd.delete('glyb') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('aspa') cmd.delete('aspb1') cmd.delete('aspb2') cmd.delete('aspb3') cmd.delete('aspb4') cmd.delete('aspb5') cmd.delete('aspb6') cmd.delete('asp') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg') def citratesynth(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'name ne2 and resn his within %s of (name og and resn ser)'%(self.range.get()*5)) cmd.select('his2', 'name ne2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('his3', 'name ce1 and resn his within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('his4', 'name ce1 and resn his within %s of (name cb and resn ser)'%(self.range.get()*6.5)) cmd.select('his5', 'name cd2 and resn his within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('his6', 'name nd1 and resn his within %s of (name og and resn ser)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*8)) cmd.select('his8', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*8.5)) cmd.select('his9', 'name o and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his10', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('his11', 'byres resn his within %s of his10'%(self.range.get()*8.2)) cmd.select('ser1', 'name og and resn ser within %s of (name ne2 and his10)'%(self.range.get()*5)) cmd.select('ser2', 'name cb and resn ser within %s of (name ne2 and his10)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name ce1 and his10)'%(self.range.get()*5.5)) cmd.select('ser4', 'name cb and resn ser within %s of (name ce1 and his10)'%(self.range.get()*6.5)) cmd.select('ser5', 'name og and resn ser within %s of (name cd2 and his10)'%(self.range.get()*6)) cmd.select('ser6', 'name og and resn ser within %s of (name nd1 and his10)'%(self.range.get()*7)) cmd.select('ser7', 'name og and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*12)) cmd.select('ser8', 'name og and resn ser within %s of (name cg and resn asp)'%(self.range.get()*12)) cmd.select('ser9', 'name og and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*12)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('his12', 'byres resn his within %s of ser'%(self.range.get()*12)) cmd.select('asp1', 'name od2 and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp2', 'name cg and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp3', 'name od1 and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nd1 and his10)'%(self.range.get()*8)) cmd.select('asp5', 'name cg and resn asp within %s of (name nd1 and his10)'%(self.range.get()*8.5)) cmd.select('asp6', 'name od2 and resn asp within %s of (name o and his10)'%(self.range.get()*5.5)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6') cmd.select('his13', 'byres resn his within %s of asp'%(self.range.get()*8.5)) cmd.select('his', 'byres his10 or (byres his11 and byres his12 and byres his13)') cmd.select('Citrate_Synth', 'his(asp(ser))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Citrate_Synth') self.cpkcitrate() cmd.orient('Citrate_Synth') cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp') def tyrosinekinase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('arg1', 'name nh1 and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('arg3', 'name cz and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('arg4', 'name ne and resn arg within %s of (name cb and resn ala)'%(self.range.get()*6)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg6', 'name nh2 and resn arg within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*6)) cmd.select('arg8', 'name cz and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg9', 'name ne and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg10', 'name ne and resn arg within %s of (name cg and resn asp)'%(self.range.get()*6.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5.5)) cmd.select('asp2', 'name cg and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5.5)) cmd.select('asp3', 'name od2 and resn asp within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('asp4', 'name od1 and resn asp within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6)) cmd.select('asp6', 'name cg and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9)) cmd.select('asp8', 'name o and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8)) cmd.select('asp9', 'name cg and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('ala1', 'name cb and resn ala within %s of (name nh1 and arg)'%(self.range.get()*5)) cmd.select('ala2', 'name cb and resn ala within %s of (name nh2 and arg)'%(self.range.get()*5.5)) cmd.select('ala3', 'name cb and resn ala within %s of (name cz and arg)'%(self.range.get()*5.5)) cmd.select('ala4', 'name cb and resn ala within %s of (name ne and arg)'%(self.range.get()*6)) cmd.select('ala5', 'name cb and resn ala within %s of (name od1 and asp)'%(self.range.get()*9)) cmd.select('ala6', 'name cb and resn ala within %s of (name o and asp)'%(self.range.get()*8)) cmd.select('ala7', 'name cb and resn ala within %s of (name cg and asp)'%(self.range.get()*8)) cmd.select('ala', 'byres ala1 and byres ala2 and byres ala3 and byres ala4 and byres ala5 and byres ala6 and byres ala7') cmd.select('SRC-Kinase', 'ala(asp(arg))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'SRC-Kinase') self.cpktyrokinase() cmd.orient('SRC-Kinase') cmd.deselect() cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') cmd.delete('ala1') cmd.delete('ala2') cmd.delete('ala3') cmd.delete('ala4') cmd.delete('ala5') cmd.delete('ala6') cmd.delete('ala7') cmd.delete('ala') def hhal(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('glu2', 'name cd and resn glu within %s of (name cb and resn cys)'%(self.range.get()*10)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name ca and resn cys)'%(self.range.get()*10)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('glu5', 'name cd and resn glu within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('glu6', 'name oe1 and resn glu within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('glu7', 'name cg and resn glu within %s of (name ca and resn phe)'%(self.range.get()*10)) cmd.select('glu8', 'name cd and resn glu within %s of (name cb and resn phe)'%(self.range.get()*10)) cmd.select('glu9', 'name ca and resn glu within %s of (name cd1 and resn phe)'%(self.range.get()*7.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9') cmd.select('cys1', 'name sg and resn cys within %s of (name nh1 and resn arg)'%(self.range.get()*6)) cmd.select('cys2', 'name cb and resn cys within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('cys3', 'name ca and resn cys within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe2 and glu)'%(self.range.get()*10)) cmd.select('cys5', 'name cb and resn cys within %s of (name cd and glu)'%(self.range.get()*10)) cmd.select('cys6', 'name ca and resn cys within %s of (name oe1 and glu)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name ca and resn phe)'%(self.range.get()*8.5)) cmd.select('cys8', 'name cb and resn cys within %s of (name cd2 and resn phe)'%(self.range.get()*9)) cmd.select('cys9', 'name sg and resn cys within %s of (name cd1 and resn phe)'%(self.range.get()*12)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('arg1', 'name nh1 and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6)) cmd.select('arg2', 'name cz and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg3', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*8)) cmd.select('arg4', 'name ne and resn arg within %s of (name oe2 and glu)'%(self.range.get()*5)) cmd.select('arg5', 'name cz and resn arg within %s of (name cd and glu)'%(self.range.get()*6)) cmd.select('arg6', 'name nh2 and resn arg within %s of (name oe1 and glu)'%(self.range.get()*5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name ce1 and resn phe)'%(self.range.get()*10.5)) cmd.select('arg8', 'name cz and resn arg within %s of (name cz and resn phe)'%(self.range.get()*11.5)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name ce2 and resn phe)'%(self.range.get()*12)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9') cmd.select('phe1', 'name ca and resn phe within %s of (name cg and glu)'%(self.range.get()*10)) cmd.select('phe2', 'name cb and resn phe within %s of (name cb and glu)'%(self.range.get()*10)) cmd.select('phe3', 'name cd1 and resn phe within %s of (name ca and glu)'%(self.range.get()*7.5)) cmd.select('phe4', 'name ce1 and resn phe within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('phe5', 'name cz and resn phe within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('phe6', 'name ce2 and resn phe within %s of (name nh1 and resn arg)'%(self.range.get()*12)) cmd.select('phe7', 'name ca and resn phe within %s of (name ca and cys)'%(self.range.get()*8.5)) cmd.select('phe8', 'name cd2 and resn phe within %s of (name cb and cys)'%(self.range.get()*9)) cmd.select('phe9', 'name cd1 and resn phe within %s of (name sg and cys)'%(self.range.get()*12)) cmd.select('phe', 'byres phe1 and byres phe2 and byres phe3 and byres phe4 and byres phe5 and byres phe6 and byres phe7 and byres phe8 and byres phe9') cmd.select('hhal', 'glu(arg(phe(cys)))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'hhal') self.cpkhhal() cmd.deselect() cmd.orient('hhal') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu') cmd.delete('phe') cmd.delete('phe1') cmd.delete('phe2') cmd.delete('phe3') cmd.delete('phe4') cmd.delete('phe5') cmd.delete('phe6') cmd.delete('phe7') cmd.delete('phe8') cmd.delete('phe9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') def betainedehydrogenase(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('cys1', 'name sg and resn cys within %s of (name od1 and resn asn)'%(self.range.get()*8.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name cg and resn asn)'%(self.range.get()*8.5)) cmd.select('cys3', 'name ca and resn cys within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*8)) cmd.select('cys5', 'name cb and resn cys within %s of (name cb and resn glu)'%(self.range.get()*9)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5') cmd.select('glu1', 'name oe1 and resn glu within %s of (name sg and cys)'%(self.range.get()*8)) cmd.select('glu2', 'name cb and resn glu within %s of (name cb and cys)'%(self.range.get()*9)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*13)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*14)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4') cmd.select('asn1', 'name nd2 and resn asn within %s of (name oe1 and glu)'%(self.range.get()*13)) cmd.select('asn2', 'name od1 and resn asn within %s of (name oe2 and glu)'%(self.range.get()*14)) cmd.select('asn3', 'name od1 and resn asn within %s of (name sg and cys)'%(self.range.get()*8.5)) cmd.select('asn4', 'name cg and resn asn within %s of (name cb and cys)'%(self.range.get()*8.5)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ca and cys)'%(self.range.get()*8.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5') cmd.select('betaine_dehydrogenase', 'cys(asn(glu))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'betaine_dehydrogenase') self.cpkbetaine() cmd.deselect() cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn') cmd.delete('cys') cmd.delete('glu') def serotoninacetyl(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('his1', 'name ne2 and resn his within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('his2', 'name ne2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('his3', 'name cd2 and resn his within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('his4', 'name cd2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*6)) cmd.select('his5', 'name ne2 and resn his within %s of (name o and resn leu)'%(self.range.get()*6)) cmd.select('his6', 'name ce1 and resn his within %s of (name cd1 and resn leu)'%(self.range.get()*10)) cmd.select('his7', 'name ce1 and resn his within %s of (name cb and resn leu)'%(self.range.get()*9)) cmd.select('his8', 'name nd1 and resn his within %s of (name og and resn ser)'%(self.range.get()*7.5)) cmd.select('his9', 'name o and resn his within %s of (name oh and resn tyr)'%(self.range.get()*10)) cmd.select('his10', 'name cb and resn his within %s of (name oh and resn tyr)'%(self.range.get()*12)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('ser1', 'name og and resn ser within %s of (name ne2 and his)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name ne2 and his)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name cd2 and his)'%(self.range.get()*5.5)) cmd.select('ser4', 'name cb and resn ser within %s of (name cd2 and his)'%(self.range.get()*6)) cmd.select('ser5', 'name og and resn ser within %s of (name nd1 and his)'%(self.range.get()*7.5)) cmd.select('ser6', 'name og and resn ser within %s of (name o and resn leu)'%(self.range.get()*5)) cmd.select('ser7', 'name og and resn ser within %s of (name cb and resn leu)'%(self.range.get()*8)) cmd.select('ser8', 'name cb and resn ser within %s of (name o and resn leu)'%(self.range.get()*5.5)) cmd.select('ser9', 'name n and resn ser within %s of (name cd2 and his)'%(self.range.get()*5.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('leu1', 'name o and resn leu within %s of (name ne2 and his)'%(self.range.get()*6)) cmd.select('leu2', 'name cd1 and resn leu within %s of (name ce1 and his)'%(self.range.get()*10)) cmd.select('leu3', 'name cb and resn leu within %s of (name ce1 and his)'%(self.range.get()*9)) cmd.select('leu4', 'name o and resn leu within %s of (name og and ser)'%(self.range.get()*5)) cmd.select('leu5', 'name cb and resn leu within %s of (name og and ser)'%(self.range.get()*8)) cmd.select('leu6', 'name o and resn leu within %s of (name cb and ser)'%(self.range.get()*5.5)) cmd.select('leu7', 'name n and resn leu within %s of (name ce1 and resn his)'%(self.range.get()*7.5)) cmd.select('leu8', 'byres leu1 and byres leu2 and byres leu3 and byres leu4 and byres leu5 and byres leu6 and byres leu7') cmd.select('leu9', 'name n and resn leu within %s of (name o and his)'%(self.range.get()*7)) cmd.select('leu10', 'name n and resn leu within %s of (name c and his)'%(self.range.get()*6.5)) cmd.select('leu11', 'name n and resn leu within %s of (name n and his)'%(self.range.get()*8)) cmd.select('leu12', 'name cd1 and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('leu13', 'name cb and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*5.5)) cmd.select('leu14', 'name cg and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('leu15', 'name cd1 and resn leu within %s of (name cz and resn tyr)'%(self.range.get()*6.5)) cmd.select('leu15b', 'name cd1 and resn leu within %s of (name ce1 and resn tyr)'%(self.range.get()*5.5)) cmd.select('leu16', 'byres leu9 and byres leu15b and byres leu10 and byres leu11 and byres leu12 and byres leu13 and byres leu14 and byres leu15') cmd.select('tyr1', 'name oh and resn tyr within %s of (name cd1 and leu16)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name cb and leu16)'%(self.range.get()*6.5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cg and leu16)'%(self.range.get()*7)) cmd.select('tyr4', 'name cz and resn tyr within %s of (name cd1 and leu16)'%(self.range.get()*6.5)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name n and his)'%(self.range.get()*10)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name c and his)'%(self.range.get()*10.2)) cmd.select('tyr7', 'name ce1 and resn tyr within %s of (name o and ser)'%(self.range.get()*16)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7') cmd.select('Serotonin_transferase', 'his(ser(leu8(leu16(tyr))))') cmd.hide('everything') cmd.show('cartoon', 'all') cmd.color('white', 'all') cmd.set('cartoon_transparency', '0.6', 'all') cmd.show('sticks', 'Serotonin_transferase') self.cpkseracetyl() cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser') cmd.delete('leu1') cmd.delete('leu2') cmd.delete('leu3') cmd.delete('leu4') cmd.delete('leu5') cmd.delete('leu6') cmd.delete('leu7') cmd.delete('leu8') cmd.delete('leu9') cmd.delete('leu10') cmd.delete('leu11') cmd.delete('leu12') cmd.delete('leu13') cmd.delete('leu14') cmd.delete('leu15') cmd.delete('leu15b') cmd.delete('leu16') cmd.delete('leu') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr') ######################################## # MOTIF SEARCH FUNCTIONS # ######################################## #Repeated definitions with view alterations removed to allow for quicker parsing def serineprotease2(self): self.deletemotif() cmd.select('asp1', 'resn asp within %s of resn his' %(self.range.get()*3)) cmd.select('asp2', 'resn asp within %s of resn ser'%(self.range.get()*7)) cmd.select('asp', 'byres asp1 and byres asp2') cmd.select('his1', 'resn his within %s of asp' %(self.range.get()*4)) cmd.select('his2', 'resn his within %s of resn ser' %(self.range.get()*4)) cmd.select('his', 'byres his1 and byres his2') cmd.select('ser1', 'name og within %s of name ne2' %(self.range.get()*3.5)) cmd.select('ser2', 'resn ser within %s of asp' %(self.range.get()*7)) cmd.select('ser', 'byres ser1 and byres ser2') cmd.select('serineprotease', 'ser(his(asp))') cmd.deselect() cmd.delete('asp') cmd.delete('his') cmd.delete('ser') cmd.delete('asp1') cmd.delete('his1') cmd.delete('ser1') cmd.delete('asp2') cmd.delete('his2') cmd.delete('ser2') def cyclinkinase2(self): self.update(self.p) self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*6.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('glu3', 'name cd and resn glu within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('glu4', 'name oe1 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu5', 'name cd and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu6', 'name oe1 and resn glu within %s of (name cd and resn lys)'%(self.range.get()*5.5)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*6)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name cg and resn lys)'%(self.range.get()*5.5)) cmd.select('glu9', 'name oe1 and resn glu within %s of (name od1 and resn asp)'%(self.range.get()*10)) cmd.select('glu10', 'name oe2 and resn glu within %s of (name od1 and resn asp)'%(self.range.get()*10)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10') cmd.select('lys1', 'name nz and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('lys2', 'name nz and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*7)) cmd.select('lys3', 'name nz and resn lys within %s of (name cd and glu)'%(self.range.get()*7)) cmd.select('lys4', 'name ce and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*6)) cmd.select('lys5', 'name ce and resn lys within %s of (name cd and resn glu)'%(self.range.get()*6)) cmd.select('lys6', 'name cd and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*5.5)) cmd.select('lys7', 'name ce and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*6)) cmd.select('lys8', 'name cg and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*5.5)) cmd.select('lys9', 'name nz and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys10', 'name nz and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*6)) cmd.select('lys11', 'name ce and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys12', 'name ce and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*6.5)) cmd.select('lys13', 'name cd and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('lys14', 'name cd and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13 and byres lys14') cmd.select('asp1', 'name od1 and resn asp within %s of (name oe1 and glu)'%(self.range.get()*10)) cmd.select('asp2', 'name od1 and resn asp within %s of (name oe2 and glu)'%(self.range.get()*10)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nz and lys)'%(self.range.get()*6)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nz and lys)'%(self.range.get()*6)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ce and lys)'%(self.range.get()*6)) cmd.select('asp6', 'name od2 and resn asp within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name cd and resn lys)'%(self.range.get()*6)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('asp9', 'name cg and resn asp within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('Cyclin_Kinase', 'lys(asp(glu))') cmd.deselect() cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys') def Blactamase2(self): self.deletemotif() cmd.select('lys1', 'name nz and resn lys within %s of (name oh and resn tyr)' %(self.range.get()*5)) cmd.select('lys2', 'name nz and resn lys within %s of (name cz and resn tyr)' %(self.range.get()*5.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name ce1 and resn tyr)' %(self.range.get()*6.5)) cmd.select('lys4', 'name nz and resn lys within %s of (name ce2 and resn tyr)' %(self.range.get()*6.5)) cmd.select('lys5', 'name ce and resn lys within %s of (name oh and resn tyr)' %(self.range.get()*5)) cmd.select('lys6', 'name ce and resn lys within %s of (name cz and resn tyr)' %(self.range.get()*6)) cmd.select('lys7', 'name nz and resn lys within %s of (name og and resn ser)' %(self.range.get()*6)) cmd.select('lys8', 'name nz and resn lys within %s of (name cb and resn ser)' %(self.range.get()*5.2)) cmd.select('lys9', 'name cb and resn lys within %s of (name cb and resn ser)' %(self.range.get()*9.2)) cmd.select('lys10', 'name ce and resn lys within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('lys11', 'name nz and resn lys within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('lys12', 'name nz and resn lys within %s of (name oe2 and resn glu)' %(self.range.get()*12.5)) cmd.select('lys13', 'name ce and resn lys within %s of (name cd and resn glu)' %(self.range.get()*11)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13') cmd.select('tyr1', 'name oh and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*5)) cmd.select('tyr2', 'name cz and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*5.5)) cmd.select('tyr3', 'name ce1 and resn tyr within %s of (name nz and lys)' %(self.range.get()*6.5)) cmd.select('tyr4', 'name ce2 and resn tyr within %s of (name nz and resn lys)' %(self.range.get()*6.5)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ce and resn lys)' %(self.range.get()*5)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name ce and resn lys)' %(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name og and resn ser)' %(self.range.get()*6)) cmd.select('tyr8', 'name cz and resn tyr within %s of (name og and resn ser)' %(self.range.get()*6.5)) cmd.select('tyr9', 'name oh and resn tyr within %s of (name cb and resn ser)' %(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name oe1 and resn glu)' %(self.range.get()*10)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name oe2 and resn glu)' %(self.range.get()*10)) cmd.select('tyr12', 'name oh and resn tyr within %s of (name cd and resn glu)' %(self.range.get()*10)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12') cmd.select('ser1', 'name cb and resn ser within %s of (name nz and lys)' %(self.range.get()*6)) cmd.select('ser2', 'name og and resn ser within %s of (name nz and resn lys)' %(self.range.get()*6)) cmd.select('ser3', 'name cb and resn ser within %s of (name cb and resn lys)' %(self.range.get()*8.2)) cmd.select('ser4', 'name og and resn ser within %s of (name cz and resn tyr)' %(self.range.get()*6.5)) cmd.select('ser5', 'name cb and resn ser within %s of (name oh and resn tyr)' %(self.range.get()*6.5)) cmd.select('ser6', 'name og and resn ser within %s of (name oh and tyr)' %(self.range.get()*6)) cmd.select('ser7', 'name og and resn ser within %s of (name oe1 and resn glu)' %(self.range.get()*12)) cmd.select('ser8', 'name og and resn ser within %s of (name oe2 and resn glu)' %(self.range.get()*12)) cmd.select('ser9', 'name cb and resn ser within %s of (name oe1 and resn glu)' %(self.range.get()*11)) cmd.select('ser10', 'name cb and resn ser within %s of (name oe2 and resn glu)' %(self.range.get()*12.5)) cmd.select('ser11', 'name og and resn ser within %s of (name cd and resn glu)' %(self.range.get()*12.5)) cmd.select('ser12', 'name cb and resn ser within %s of (name cd and resn glu)' %(self.range.get()*11.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10 and byres ser11 and byres ser12') cmd.select('glu1', 'name oe1 and resn glu within %s of (name ce and lys)' %(self.range.get()*8.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)' %(self.range.get()*9.5)) cmd.select('glu3', 'name oe2 and resn glu within %s of (name nz and resn lys)' %(self.range.get()*11.2)) cmd.select('glu4', 'name cd and resn glu within %s of (name ce and resn lys)' %(self.range.get()*10.6)) cmd.select('glu5', 'name oe1 and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*8.7)) cmd.select('glu6', 'name oe2 and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*9.7)) cmd.select('glu7', 'name cd and resn glu within %s of (name oh and resn tyr)' %(self.range.get()*9.6)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name og and ser)' %(self.range.get()*10.5)) cmd.select('glu9', 'name oe2 and resn glu within %s of (name og and ser)' %(self.range.get()*10.5)) cmd.select('glu10', 'name oe1 and resn glu within %s of (name cb and resn ser)' %(self.range.get()*10)) cmd.select('glu11', 'name oe2 and resn glu within %s of (name cb and resn ser)' %(self.range.get()*11.8)) cmd.select('glu12', 'name cd and resn glu within %s of (name og and resn ser)' %(self.range.get()*11.8)) cmd.select('glu13', 'name cd and resn glu within %s of (name cb and resn ser)' %(self.range.get()*11)) cmd.select('glu14', 'name oe1 and resn glu within %s of (name cg and resn tyr)' %(self.range.get()*7.4)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11 and byres glu12 and byres glu13 and byres glu14') cmd.select('lactamase', 'ser(tyr(glu(lys)))') cmd.deselect cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr2') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser11') cmd.delete('ser12') cmd.delete('ser') cmd.delete('glu') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu12') cmd.delete('glu13') cmd.delete('glu14') cmd.deselect() def superoxide2(self): self.deletemotif() cmd.select('his1', 'byres resn his within %s of elem cu'%(self.range.get()*4)) cmd.select('arg1', 'byres resn arg within %s of elem cu'%(self.range.get()*6)) cmd.select('stuff', 'his1 and (byres elem zn around %s)'%(self.range.get()*4)) cmd.select('stuff1', 'arg1 and (byres elem zn around %s)'%(self.range.get()*6)) cmd.select('stuff2', 'byres elem cu around %s and his1'%(self.range.get()*4)) cmd.select('stuff3', 'byres elem cu around %s and arg1'%(self.range.get()*6)) cmd.select('stuff4', 'stuff and stuff1 and stuff2 and stuff3') cmd.select('superoxide', 'byres his1(arg1(stuff4))') cmd.deselect() cmd.delete('his1') cmd.delete('arg1') cmd.delete('stuff') cmd.delete('stuff1') cmd.delete('stuff2') cmd.delete('stuff3') cmd.delete('stuff4') def metalloprotease2(self): self.deletemotif() cmd.select('zn', 'elem zn') cmd.select('metalloprotease', 'zn(byres zn around %s)'%(self.range.get()*5)) cmd.delete('zn') cmd.deselect() def tyrophos2(self): self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() self.deletemotif() cmd.hide('everything') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('arg3', 'name ne and resn arg within %s of (name cb and resn asp)'%(self.range.get()*6.5)) cmd.select('arg4', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*7)) cmd.select('arg5', 'name nh1 and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg6', 'name ne and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name og and resn ser)'%(self.range.get()*10)) cmd.select('arg8', 'name nh1 and resn arg within %s of (name cb and resn ser)'%(self.range.get()*11.2)) cmd.select('arg9', 'name ne and resn arg within %s of (name ca and resn ser)'%(self.range.get()*9)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg6 and byres arg7 and byres arg8 and byres arg9') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh1 and arg)'%(self.range.get()*7)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('asp3', 'name cb and resn asp within %s of (name ne and arg)'%(self.range.get()*6.5)) cmd.select('asp4', 'name od2 and resn asp within %s of (name c and resn ser)'%(self.range.get()*11)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ca and resn ser)'%(self.range.get()*12)) cmd.select('asp6', 'name cb and resn asp within %s of (name cb and resn ser)'%(self.range.get()*9.2)) cmd.select('asp7', 'name od1 and resn asp within %s of (name c and resn cys)'%(self.range.get()*12)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*11)) cmd.select('asp9', 'name cb and resn asp within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('cys1', 'name ca and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys3', 'name sg and resn cys within %s of (name ca and resn ser)'%(self.range.get()*6)) cmd.select('cys4', 'name c and resn cys within %s of (name od1 and asp)'%(self.range.get()*12)) cmd.select('cys5', 'name cb and resn cys within %s of (name od2 and asp)'%(self.range.get()*11)) cmd.select('cys6', 'name sg and resn cys within %s of (name cb and asp)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name nh1 and arg)'%(self.range.get()*7)) cmd.select('cys9', 'name sg and resn cys within %s of (name ne and arg)'%(self.range.get()*6.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name nh2 and arg)'%(self.range.get()*10)) cmd.select('ser2', 'name cb and resn ser within %s of (name nh1 and arg)'%(self.range.get()*11.2)) cmd.select('ser3', 'name ca and resn ser within %s of (name ne and arg)'%(self.range.get()*9)) cmd.select('ser4', 'name c and resn ser within %s of (name od2 and asp)'%(self.range.get()*11)) cmd.select('ser5', 'name ca and resn ser within %s of (name od1 and asp)'%(self.range.get()*12)) cmd.select('ser6', 'name cb and resn ser within %s of (name cb and asp)'%(self.range.get()*9.2)) cmd.select('ser7', 'name og and resn ser within %s of (name ca and cys)'%(self.range.get()*6.5)) cmd.select('ser8', 'name cb and resn ser within %s of (name cb and cys)'%(self.range.get()*7)) cmd.select('ser9', 'name ca and resn ser within %s of (name sg and cys)'%(self.range.get()*6)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('tyrophos', 'ser(asp(arg(cys)))') tycount = cmd.index('tyrophos') atcount = len(tycount) if(atcount < 1): cmd.hide('everything') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('arg3', 'name ne and resn arg within %s of (name cb and resn asp)'%(self.range.get()*6.5)) cmd.select('arg4', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*7)) cmd.select('arg5', 'name nh1 and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg6', 'name ne and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg6') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh1 and resn arg)'%(self.range.get()*7)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*7)) cmd.select('asp3', 'name cb and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name c and resn cys)'%(self.range.get()*12)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*11)) cmd.select('asp9', 'name cb and resn asp within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp7 and byres asp8 and byres asp9') cmd.select('cys4', 'name c and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*12)) cmd.select('cys5', 'name cb and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*11)) cmd.select('cys6', 'name sg and resn cys within %s of (name cb and resn asp)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name nh2 and resn arg)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name nh1 and resn arg)'%(self.range.get()*7)) cmd.select('cys9', 'name sg and resn cys within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('cys', 'byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('tyrophos', '(asp(arg(cys)))') cmd.delete('arg') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.orient('tyrophos') cmd.deselect() else: cmd.delete('arg') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.orient('tyrophos') cmd.deselect() def carbanhyd2(self): self.deletemotif() cmd.select('zn', 'elem zn') cmd.select('his', 'resn his within %s of zn'%(self.range.get()*5)) cmd.select('carbonicanhydrase', 'byres his or zn') cmd.delete('zn') cmd.delete('his') cmd.deselect() def betainedehydrogenase2(self): self.deletemotif() cmd.select('cys1', 'name sg and resn cys within %s of (name od1 and resn asn)'%(self.range.get()*8.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name cg and resn asn)'%(self.range.get()*8.5)) cmd.select('cys3', 'name ca and resn cys within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*8)) cmd.select('cys5', 'name cb and resn cys within %s of (name cb and resn glu)'%(self.range.get()*9)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5') cmd.select('glu1', 'name oe1 and resn glu within %s of (name sg and cys)'%(self.range.get()*8)) cmd.select('glu2', 'name cb and resn glu within %s of (name cb and cys)'%(self.range.get()*9)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*13)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*14)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4') cmd.select('asn1', 'name nd2 and resn asn within %s of (name oe1 and glu)'%(self.range.get()*13)) cmd.select('asn2', 'name od1 and resn asn within %s of (name oe2 and glu)'%(self.range.get()*14)) cmd.select('asn3', 'name od1 and resn asn within %s of (name sg and cys)'%(self.range.get()*8.5)) cmd.select('asn4', 'name cg and resn asn within %s of (name cb and cys)'%(self.range.get()*8.5)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ca and cys)'%(self.range.get()*8.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5') cmd.select('betaine_dehydrogenase', 'cys(asn(glu))') cmd.deselect() cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn') cmd.delete('cys') cmd.delete('glu') def paplike2(self): self.deletemotif() cmd.select('gln1', 'name ne2 and resn gln within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('gln2', 'name cd and resn gln within %s of (name ce1 and resn his)'%(self.range.get()*6.7)) cmd.select('gln3', 'name oe1 and resn gln within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('gln4', 'name ne2 and resn gln within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('gln5', 'name oe1 and resn gln within %s of (name sg and resn cys)'%(self.range.get()*6.7)) cmd.select('gln', 'byres gln1 and byres gln2 and byres gln3 and byres gln4 and byres gln5') cmd.select('his1', 'name ne2 and resn his within %s of (name ne2 and gln)'%(self.range.get()*7)) cmd.select('his2', 'name ce1 and resn his within %s of (name cd and gln)'%(self.range.get()*6.7)) cmd.select('his3', 'name nd1 and resn his within %s of (name oe1 and gln)'%(self.range.get()*7)) cmd.select('his4', 'name ce1 and resn his within %s of (name cb and resn cys)'%(self.range.get()*5.7)) cmd.select('his5', 'name nd1 and resn his within %s of (name sg and resn cys)'%(self.range.get()*6)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5') cmd.select('cys1', 'name cb and resn cys within %s of (name ce1 and his)'%(self.range.get()*5.7)) cmd.select('cys2', 'name sg and resn cys within %s of (name nd1 and his)'%(self.range.get()*6)) cmd.select('cys3', 'name cb and resn cys within %s of (name ne2 and gln)'%(self.range.get()*5.5)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe1 and gln)'%(self.range.get()*6.7)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4') cmd.select('paplike', 'gln(his(cys))') cmd.delete('his') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('gln') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln4') cmd.delete('gln5') cmd.orient('paplike') cmd.deselect() def zincfinger2(self): self.deletemotif() cmd.select('zn1', 'elem zn') xm = cmd.index('zn1') nm = len(xm) if(nm < 1): cmd.delete('zn1') objects = cmd.get_names('all') if 'zn1' in objects: cmd.select('zn1', 'elem zn') cmd.select('his', 'resn his') cmd.select('cys', 'resn cys') cmd.select('cys1', 'resn cys around %s'%(self.range.get()*4)) cmd.select('Zinc_finger', '(resn cys or resn his(and byres cys1))') cmd.delete('zn1') cmd.delete('his') cmd.delete('cys') cmd.delete('cys1') cmd.deselect() def aminotransferase2(self): self.deletemotif() cmd.select('asp1', 'name od1 and resn asp within %s of (name cb and resn his)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name cg and resn his)'%(self.range.get()*6)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('asp4', 'name cg and resn asp within %s of (name cb and resn his)'%(self.range.get()*6.5)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asp6', 'name od1 and resn asp within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asp7', 'name od2 and resn asp within %s of (name nz and resn lys)'%(self.range.get()*9)) cmd.select('asp8', 'name cg and resn asp within %s of (name nz and resn lys)'%(self.range.get()*9)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp8') cmd.select('his1', 'name cb and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('his2', 'name cg and resn his within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('his3', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('his4', 'name cb and resn his within %s of (name cg and asp)'%(self.range.get()*6.5)) cmd.select('his5', 'name ne2 and resn his within %s of (name od1 and asp)'%(self.range.get()*8)) cmd.select('his6', 'name cd2 and resn his within %s of (name od1 and asp)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*8)) cmd.select('his9', 'name ce1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('lys1', 'name nz and resn lys within %s of (name od2 and asp)'%(self.range.get()*9)) cmd.select('lys2', 'name nz and resn lys within %s of (name cg and asp)'%(self.range.get()*9)) cmd.select('lys3', 'name nz and resn lys within %s of (name nd1 and his)'%(self.range.get()*7.5)) cmd.select('lys4', 'name nz and resn lys within %s of (name ne2 and his)'%(self.range.get()*8)) cmd.select('lys5', 'name nz and resn lys within %s of (name ce1 and his)'%(self.range.get()*7)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5') cmd.select('Aminotransferase', 'asp(his(lys))') cmd.deselect() cmd.delete('his') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('lys') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('asp') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') def fisomerase2(self): self.deletemotif() cmd.select('his', 'elem mn around %s(elem mn)'%(self.range.get()*5)) cmd.select('fucoseisomerase', 'byres resn asp and his(byres resn glu and his(elem mn))') cmd.deselect() cmd.delete('his') def glutamine_amidotransferase2(self): self.deletemotif() cmd.select('his1', 'name ND1 within %s of name OE2'%(self.range.get()*3)) cmd.select('his2', 'name NE2 within %s of name SG'%(self.range.get()*3.5)) cmd.select('his', 'byres his1 and byres his2') cmd.select('glu1', 'resn glu within %s of his'%(self.range.get()*3.2)) cmd.select('glu2', 'resn glu within %s of resn cys'%(self.range.get()*7)) cmd.select('glu', 'byres glu1 and byres glu2') cmd.select('cys1', 'resn cys within %s of his'%(self.range.get()*3.5)) cmd.select('cys2', 'resn cys within %s of glu'%(self.range.get()*7)) cmd.select('cys', 'byres cys1 and byres cys2') cmd.select('glu_amidotransferase', 'cys(his(glu))') cmd.deselect() cmd.delete('his') cmd.delete('his1') cmd.delete('his2') cmd.delete('glu') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') def dnaligase2(self): self.deletemotif() cmd.select('amp1', 'resn amp') cmd.select('atp1', 'resn atp') xp = cmd.index('amp1') np = len(xp) if(np < 1): cmd.delete('amp1') xtp = cmd.index('atp1') ntp = len(xtp) if(ntp < 1): cmd.delete('atp1') objects = cmd.get_names('all') if 'amp1' in objects: cmd.select('ramp1', 'byres resn amp around %s'%(self.range.get()*7.4)) cmd.select('lys1', 'byres resn lys and ramp1') cmd.select('ramp2', 'byres resn amp around %s'%(self.range.get()*7)) cmd.select('ramp3', 'byres resn amp around %s'%(self.range.get()*5.3)) cmd.select('asp1', 'ramp3 and(byres resn asp within %s of lys1)'%(self.range.get()*3)) cmd.select('arg1', 'ramp2 and(byres resn arg within %s of asp1)'%(self.range.get()*5)) cmd.select('Ligase', 'byres lys1(amp1(byres arg1(byres asp1)))') cmd.deselect() elif 'atp1' in objects: cmd.select('ratp1', 'byres resn atp around %s'%(self.range.get()*7.4)) cmd.select('lys1', 'byres resn lys and ratp1') cmd.select('ratp2', 'byres resn atp around %s'%(self.range.get()*7)) cmd.select('ratp3', 'byres resn atp around %s'%(self.range.get()*5.3)) cmd.select('asp1', 'ratp3 and(byres resn asp within %s of lys1)'%(self.range.get()*3)) cmd.select('arg1', 'ratp2 and(byres resn arg within %s of asp1)'%(self.range.get()*5)) cmd.select('Ligase', 'byres lys1(atp1(byres arg1(byres asp1)))') cmd.deselect() elif 'amp1' or 'atp1' not in objects: cmd.select('asp1', 'name OD2 within %s of name NE'%(self.range.get()*5.5)) cmd.select('arg1', 'name NE within %s of name OD2'%(self.range.get()*5.5)) cmd.select('lys1', 'name NZ within %s of name OD2'%(self.range.get()*9)) cmd.select('lys4', 'name NZ within %s of name NH2'%(self.range.get()*10)) cmd.select('arg', 'byres resn arg and arg1') cmd.select('asp', 'byres resn asp and asp1') cmd.select('lys3', 'byres resn lys and lys1 and lys4') cmd.select('Ligase', 'byres arg(asp(lys3))') cmd.deselect() cmd.orient('Ligase') cmd.delete('asp1') cmd.delete('arg1') cmd.delete('lys1') cmd.delete('arg') cmd.delete('asp') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys') cmd.delete('ratp1') cmd.delete('ratp2') cmd.delete('ratp3') cmd.delete('atp1') cmd.delete('ramp1') cmd.delete('ramp2') cmd.delete('ramp3') cmd.delete('lys') cmd.delete('amp1') def thymidinekinase2(self): self.deletemotif() cmd.select('glu1', 'name OE1 and resn glu within %s of name NH2 and resn arg'%(self.range.get()*5)) cmd.select('glu2', 'resn glu and name OE2 within %s of name NE and resn arg'%(self.range.get()*5)) cmd.select('glu3', 'resn glu and name OE1 within %s of name NH1 and resn arg'%(self.range.get()*6)) cmd.select('glu4', 'resn glu and name OE1 within %s of name NE and resn arg'%(self.range.get()*6)) cmd.select('glu5', 'resn glu and name OE2 within %s of name NH2 and resn arg'%(self.range.get()*5.5)) cmd.select('glu6', 'resn glu and name oe1 within %s of name CZ and resn arg'%(self.range.get()*5)) cmd.select('glu7', 'resn glu and name oe2 within %s of name CZ and resn arg'%(self.range.get()*5)) cmd.select('glu8', 'resn glu and name oe1 within %s of name CD and resn arg'%(self.range.get()*5.8)) cmd.select('glu9', 'resn glu and name oe2 within %s of name CD and resn arg'%(self.range.get()*5.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres resn glu') cmd.select('arg1', 'resn arg and name NH1 within %s of name OE2 and glu'%(self.range.get()*6)) cmd.select('arg2', 'resn arg and name NE within %s of name OE2 and glu'%(self.range.get()*5.2)) cmd.select('arg3', 'resn arg and name NH1 within %s of name oe1 and glu'%(self.range.get()*6)) cmd.select('arg4', 'resn arg and name ne within %s of name oe1 and resn glu'%(self.range.get()*6.5)) cmd.select('arg5', 'resn arg and name nh2 within %s of name oe2 and resn glu'%(self.range.get()*5.8)) cmd.select('arg', 'byres resn arg and byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5') cmd.select('gly1', 'byres resn gly within %s of arg'%(self.range.get()*6.2)) cmd.select('gly2', 'byres resn gly within %s of glu'%(self.range.get()*9)) cmd.select('gly', 'byres resn gly and byres gly1 and byres gly2') cmd.select('glu10', 'byres glu within 10 of gly') cmd.select('arg10', 'byres arg within 9 of gly') cmd.select('Tkinase', 'glu10(arg10(gly))') cmd.deselect() cmd.orient('Tkinase') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg10') cmd.delete('arg') cmd.delete('gly1') cmd.delete('gly2') cmd.delete('gly') cmd.delete('thm1') cmd.delete('tmp1') cmd.delete('tdp1') cmd.delete('ttp1') def oglycosyl2(self): self.deletemotif() cmd.select('tyr', 'name oh within %s of name oe1'%(self.range.get()*3.5)) cmd.select('glu', 'resn glu within %s of tyr'%(self.range.get()*8)) cmd.select('o-glycosyl', 'byres tyr or byres glu') cmd.delete('tyr') cmd.delete('glu') cmd.deselect() def carboncarbon2(self): self.deletemotif() cmd.select('asp1', 'name od1 within %s of name nz'%(self.range.get()*3.5)) cmd.select('asp2', 'resn asp within %s of name ne2'%(self.range.get()*6)) cmd.select('asp', 'byres asp1 and byres asp2') cmd.select('lys1', 'name nz within %s of asp'%(self.range.get()*6)) cmd.select('lys2', 'resn lys within %s of resn his'%(self.range.get()*8)) cmd.select('lys', 'byres lys1 and byres lys2') cmd.select('his1', 'name ne2 within %s of name nz'%(self.range.get()*6)) cmd.select('his2', 'resn his within %s of lys'%(self.range.get()*6)) cmd.select('his3', 'resn his within %s of asp'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3') cmd.select('carboncarbon', 'asp(lys(his))') cmd.delete('his1') cmd.delete('lys1') cmd.delete('glu1') cmd.deselect() cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his') def peroxidase2(self): self.deletemotif() cmd.select('asn1', 'name od1 within %s of name nd1'%(self.range.get()*8)) cmd.select('asn2', 'name od1 within %s of name ne2'%(self.range.get()*6)) cmd.select('asn3', 'name nd2 within %s of name nd1'%(self.range.get()*10)) cmd.select('asn4', 'name nd2 within %s of name ne2'%(self.range.get()*8)) cmd.select('asn5', 'name od1 within %s of name nh2'%(self.range.get()*7)) cmd.select('asn6', 'name od1 within %s of name nh1'%(self.range.get()*8.6))#measure more cmd.select('asn7', 'name od1 within %s of name ne'%(self.range.get()*8)) cmd.select('asn8', 'name nd2 within %s of name nh2'%(self.range.get()*9)) cmd.select('asn9', 'name nd2 within %s of name nh1'%(self.range.get()*11))# cmd.select('asn10', 'name nd2 within %s of name ne'%(self.range.get()*9.8)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10') cmd.select('his1', 'name nd1 within %s of name od1'%(self.range.get()*5)) cmd.select('his2','name ne2 within %s of name od1'%(self.range.get()*5)) cmd.select('his3', 'name nd1 within %s of name nd2'%(self.range.get()*8))# cmd.select('his4', 'name ne2 within %s of name nd2'%(self.range.get()*8.5))# cmd.select('his5', 'name ne2 within %s of name ne'%(self.range.get()*5.8)) cmd.select('his6', 'name ne2 within %s of name nh2'%(self.range.get()*6))# cmd.select('his7', 'name ne2 within %s of name nh1'%(self.range.get()*8.2))# cmd.select('his8', 'name nd1 within %s of name nh1'%(self.range.get()*7.2))# cmd.select('his9', 'name nd1 within %s of name nh2'%(self.range.get()*5.8)) cmd.select('his10', 'name nd1 within %s of name ne'%(self.range.get()*7)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('arg1', 'name nh2 within %s of name od1'%(self.range.get()*7.5)) cmd.select('arg2', 'name nh2 within %s of name nd2'%(self.range.get()*9.5)) cmd.select('arg3', 'name nh2 within %s of name ne2'%(self.range.get()*6))# cmd.select('arg4', 'name nh2 within %s of name nd1'%(self.range.get()*6)) cmd.select('arg5', 'name nh1 within %s of name od1'%(self.range.get()*8))# cmd.select('arg6', 'name nh1 within %s of name nd2'%(self.range.get()*10)) cmd.select('arg7', 'name nh1 within %s of name ne2'%(self.range.get()*8))# cmd.select('arg8', 'name nh1 within %s of name nd1'%(self.range.get()*7.4))# cmd.select('arg9', 'name ne within %s of name od1'%(self.range.get()*7.2)) cmd.select('arg10', 'name ne within %s of name nd2'%(self.range.get()*8.9)) cmd.select('arg11', 'name ne within %s of name ne2'%(self.range.get()*5.9)) cmd.select('arg12', 'name ne within %s of name nd1'%(self.range.get()*6)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byres arg11 and byres arg12') cmd.select('Peroxidase', 'asn(his(arg))') cmd.deselect() cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg12') cmd.delete('arg') def trioseisomerase2(self): self.deletemotif() cmd.select('lys1', 'name nz and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('lys2', 'name nz and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('lys4', 'name ce and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys5', 'name ce and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys6', 'name ce and resn lys within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('lys7', 'name cd and resn lys within %s of (name od1 and resn asn)'%(self.range.get()*6.2)) cmd.select('lys8', 'name cd and resn lys within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('lys9', 'name cd and resn lys within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('lys10', 'name nz and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('lys11', 'name nz and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7.5)) cmd.select('lys12', 'name nz and resn lys within %s of (name ce1 and resn his)'%(self.range.get()*6.7)) cmd.select('lys13', 'name nz and resn lys within %s of (name cd2 and resn his)'%(self.range.get()*7.5)) cmd.select('lys14', 'name nz and resn lys within %s of (name cg and resn his)'%(self.range.get()*8)) cmd.select('lys15', 'name ce and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*6.2)) cmd.select('lys16', 'name ce and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7.6)) cmd.select('lys17', 'name ce and resn lys within %s of (name ce1 and resn his)'%(self.range.get()*6.6)) cmd.select('lys18', 'name ce and resn lys within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('lys19', 'name ce and resn lys within %s of (name cg and resn his)'%(self.range.get()*7.5)) cmd.select('lys20', 'name nz and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*8.5)) cmd.select('lys21', 'name nz and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*10)) cmd.select('lys22', 'name nz and resn lys within %s of (name cd and resn glu)'%(self.range.get()*9.5)) cmd.select('lys23', 'name ce and resn lys within %s of (name oe2 and resn glu)'%(self.range.get()*9)) cmd.select('lys24', 'name ce and resn lys within %s of (name oe1 and resn glu)'%(self.range.get()*10.2)) cmd.select('lys25', 'name ce and resn lys within %s of (name cd and resn glu)'%(self.range.get()*10)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9 and byres lys10 and byres lys11 and byres lys12 and byres lys13 and byres lys14 and byres lys15 and byres lys16 and byres lys17 and byres lys18 and byres lys19 and byres lys20 and byres lys21 and byres lys22 and byres lys23 and byres lys24 and byres lys25') cmd.select('asn1', 'name od1 and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn2', 'name nd2 and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn3', 'name cg and resn asn within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn6', 'name cg and resn asn within %s of (name ce and resn lys)'%(self.range.get()*6.5)) cmd.select('asn7', 'name od1 and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.2)) cmd.select('asn8', 'name cg and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name cd and resn lys)'%(self.range.get()*6.5)) cmd.select('asn10', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*6.3)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*6.2)) cmd.select('asn12', 'name nd2 and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*7.3)) cmd.select('asn13', 'name nd2 and resn asn within %s of (name nd1 and resn his)'%(self.range.get()*8)) cmd.select('asn14', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn15', 'name od1 and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*9.2)) cmd.select('asn16', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*8.3)) cmd.select('asn17', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7.5)) cmd.select('asn18', 'name cg and resn asn within %s of (name ce1 and resn his)'%(self.range.get()*8.5)) cmd.select('asn19', 'name cg and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7.5)) cmd.select('asn20', 'name nd2 and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*9)) cmd.select('asn21', 'name nd2 and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*10.5)) cmd.select('asn22', 'name nd2 and resn asn within %s of (name cd and resn glu)'%(self.range.get()*10.2)) cmd.select('asn23', 'name cg and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*10)) cmd.select('asn24', 'name cg and resn asn within %s of (name cd and resn glu)'%(self.range.get()*11)) cmd.select('asn25', 'name cg and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*11.3)) cmd.select('asn26', 'name od1 and resn asn within %s of (name oe2 and resn glu)'%(self.range.get()*11)) cmd.select('asn27', 'name od1 and resn asn within %s of (name cd and resn glu)'%(self.range.get()*11)) cmd.select('asn28', 'name od1 and resn asn within %s of (name oe1 and resn glu)'%(self.range.get()*12)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11 and byres asn12 and byres asn13 and byres asn14 and byres asn15 and byres asn16 and byres asn17 and byres asn18 and byres asn19 and byres asn20 and byres asn21 and byres asn22 and byres asn23 and byres asn24 and byres asn25 and byres asn26 and byres asn27 and byres asn28') cmd.select('glu1', 'name oe2 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*8.5)) cmd.select('glu2', 'name oe1 and resn glu within %s of (name nz and resn lys)'%(self.range.get()*10)) cmd.select('glu3', 'name cd and resn glu within %s of (name nz and resn lys)'%(self.range.get()*9.5)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*9)) cmd.select('glu5', 'name oe1 and resn glu within %s of (name ce and resn lys)'%(self.range.get()*10.2)) cmd.select('glu6', 'name cd and resn glu within %s of (name ce and resn lys)'%(self.range.get()*10)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*9)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*10.5)) cmd.select('glu9', 'name cd and resn glu within %s of (name nd2 and resn asn)'%(self.range.get()*10.2)) cmd.select('glu10', 'name oe2 and resn glu within %s of (name cg and resn asn)'%(self.range.get()*10)) cmd.select('glu11', 'name cd and resn glu within %s of (name cg and resn asn)'%(self.range.get()*11)) cmd.select('glu12', 'name oe1 and resn glu within %s of (name cg and resn asn)'%(self.range.get()*11.3)) cmd.select('glu13', 'name oe2 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('glu14', 'name cd and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('glu15', 'name oe1 and resn glu within %s of (name od1 and resn asn)'%(self.range.get()*12)) cmd.select('glu16', 'name oe2 and resn glu within %s of (name ne2 and resn his)'%(self.range.get()*5.6)) cmd.select('glu17', 'name oe2 and resn glu within %s of (name cd2 and resn his)'%(self.range.get()*6.5)) cmd.select('glu18', 'name oe2 and resn glu within %s of (name ce1 and resn his)'%(self.range.get()*5.8)) cmd.select('glu19', 'name oe2 and resn glu within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('glu20', 'name oe2 and resn glu within %s of (name cg and resn his)'%(self.range.get()*6.6)) cmd.select('glu21', 'name oe1 and resn glu within %s of (name ne2 and resn his)'%(self.range.get()*6.6)) cmd.select('glu22', 'name oe1 and resn glu within %s of (name cd2 and resn his)'%(self.range.get()*6.5)) cmd.select('glu23', 'name oe1 and resn glu within %s of (name ce1 and resn his)'%(self.range.get()*5.8)) cmd.select('glu24', 'name oe1 and resn glu within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('glu25', 'name oe1 and resn glu within %s of (name cg and resn his)'%(self.range.get()*6.6)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11 and byres glu12 and byres glu13 and byres glu14 and byres glu15 and byres glu16 and byres glu17 and byres glu18 and byres glu19 and byres glu20 and byres glu21 and byres glu22 and byres glu23 and byres glu24 and byres glu25') cmd.select('his1', 'name ne2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*6.5)) cmd.select('his2', 'name nd1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his3', 'name ce1 and resn his within %s of (name nz and resn lys)'%(self.range.get()*6.7)) cmd.select('his4', 'name cd2 and resn his within %s of (name nz and resn lys)'%(self.range.get()*7.5)) cmd.select('his5', 'name cg and resn his within %s of (name nz and resn lys)'%(self.range.get()*8)) cmd.select('his6', 'name ne2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*6.2)) cmd.select('his7', 'name nd1 and resn his within %s of (name ce and resn lys)'%(self.range.get()*7.6)) cmd.select('his8', 'name ce1 and resn his within %s of (name ce and resn lys)'%(self.range.get()*6.6)) cmd.select('his9', 'name cd2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*7)) cmd.select('his10', 'name cg and resn his within %s of (name ce and resn lys)'%(self.range.get()*7.5)) cmd.select('his11', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*6.3)) cmd.select('his12', 'name cd2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*6.2)) cmd.select('his13', 'name ce1 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*7.3)) cmd.select('his14', 'name nd1 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his15', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*8)) cmd.select('his16', 'name ce1 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*9.2)) cmd.select('his17', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*8.3)) cmd.select('his18', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('his19', 'name ce1 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8.5)) cmd.select('his20', 'name cd2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*7.5)) cmd.select('his21', 'name ne2 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*5.6)) cmd.select('his22', 'name cd2 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('his23', 'name ce1 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*5.8)) cmd.select('his24', 'name nd1 and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('his25', 'name cg and resn his within %s of (name oe2 and resn glu)'%(self.range.get()*6.6)) cmd.select('his26', 'name ne2 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.6)) cmd.select('his27', 'name cd2 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('his28', 'name ce1 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*5.8)) cmd.select('his29', 'name nd1 and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('his30', 'name cg and resn his within %s of (name oe1 and resn glu)'%(self.range.get()*6.6)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13 and byres his14 and byres his15 and byres his16 and byres his17 and byres his18 and byres his19 and byres his20 and byres his21 and byres his22 and byres his23 and byres his24 and byres his25 and byres his26 and byres his27 and byres his28 and byres his29 and byres his30') cmd.select('TrioseIsomerase', 'glu(his(asn(lys)))') cmd.deselect() cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn12') cmd.delete('asn13') cmd.delete('asn14') cmd.delete('asn15') cmd.delete('asn16') cmd.delete('asn17') cmd.delete('asn18') cmd.delete('asn19') cmd.delete('asn20') cmd.delete('asn21') cmd.delete('asn22') cmd.delete('asn23') cmd.delete('asn24') cmd.delete('asn25') cmd.delete('asn26') cmd.delete('asn27') cmd.delete('asn28') cmd.delete('asn') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his14') cmd.delete('his15') cmd.delete('his16') cmd.delete('his17') cmd.delete('his18') cmd.delete('his19') cmd.delete('his20') cmd.delete('his21') cmd.delete('his22') cmd.delete('his23') cmd.delete('his24') cmd.delete('his25') cmd.delete('his26') cmd.delete('his27') cmd.delete('his28') cmd.delete('his29') cmd.delete('his30') cmd.delete('his') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu12') cmd.delete('glu13') cmd.delete('glu14') cmd.delete('glu15') cmd.delete('glu16') cmd.delete('glu17') cmd.delete('glu18') cmd.delete('glu19') cmd.delete('glu20') cmd.delete('glu21') cmd.delete('glu22') cmd.delete('glu23') cmd.delete('glu24') cmd.delete('glu25') cmd.delete('glu') cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys10') cmd.delete('lys11') cmd.delete('lys12') cmd.delete('lys13') cmd.delete('lys14') cmd.delete('lys15') cmd.delete('lys16') cmd.delete('lys17') cmd.delete('lys18') cmd.delete('lys19') cmd.delete('lys20') cmd.delete('lys21') cmd.delete('lys22') cmd.delete('lys23') cmd.delete('lys24') cmd.delete('lys25') cmd.delete('lys') def alcoholdehyd2(self): self.deletemotif() cmd.select('tyr1', 'name cd1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*5)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*8)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name nz and resn lys)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('tyr5', 'name ce2 and resn tyr within %s of (name cg and resn lys)'%(self.range.get()*6)) cmd.select('tyr6', 'name cg and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7') cmd.select('asn1', 'name nd2 and resn asn within %s of (name cd1 and tyr)'%(self.range.get()*5)) cmd.select('asn2', 'name nd2 and resn asn within %s of (name oh and tyr)'%(self.range.get()*7)) cmd.select('asn3', 'name od1 and resn asn within %s of (name oh and tyr)'%(self.range.get()*7)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ce1 and tyr)'%(self.range.get()*6)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ce and resn lys)'%(self.range.get()*5.5)) cmd.select('asn6', 'name od1 and resn asn within %s5 of (name nz and resn lys)'%(self.range.get()*5.5)) cmd.select('asn7', 'name nd2 and resn asn within %s of (name og and resn ser)'%(self.range.get()*10)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7') cmd.select('lys1', 'name nz and resn lys within %s of (name od1 and asn)'%(self.range.get()*6)) cmd.select('lys2', 'name ce and resn lys within %s of (name nd2 and asn)'%(self.range.get()*6.5)) cmd.select('lys3', 'name nz and resn lys within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('lys4', 'name ce and resn lys within %s of (name cz and tyr)'%(self.range.get()*6)) cmd.select('lys4', 'name nz and resn lys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('lys5', 'name ce and resn lys within %s of (name og and resn ser)'%(self.range.get()*7)) cmd.select('lys6', 'name cg and resn lys within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('lys7', 'name cd and resn lys within %s of (name cb and resn ser)'%(self.range.get()*6)) cmd.select('lys8', 'name cd and resn lys within %s of (name cb and resn asn)'%(self.range.get()*7)) cmd.select('lys9', 'name ce and resn lys within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9') cmd.select('ser1', 'name og and resn ser within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('ser2', 'name og and resn ser within %s of (name ce2 and tyr)'%(self.range.get()*6)) cmd.select('ser3', 'name og and resn ser within %s of (name nz and lys)'%(self.range.get()*8)) cmd.select('ser4', 'name cb and resn ser within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('ser5', 'name cb and resn ser within %s of (name cd and lys)'%(self.range.get()*6)) cmd.select('ser6', 'name cb and resn ser within %s of (name od1 and asn)'%(self.range.get()*10)) cmd.select('ser7', 'name ca and resn ser within %s of (name nd2 and asn)'%(self.range.get()*10)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7') cmd.select('alcoholdehyd','ser(tyr(lys(asn)))') cmd.deselect() cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('asn') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('lys') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys1') cmd.delete('ser') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') def aldoreductase2(self): self.deletemotif() cmd.select('lys1', 'name cd and resn lys within %s of (name cg and resn his)'%(self.range.get()*6)) cmd.select('lys2', 'name ce and resn lys within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('lys3', 'name cd and resn lys within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('lys4', 'name nz and resn lys within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('lys5', 'name nz and resn lys within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('lys6', 'name cg and resn lys within %s of (name cz and resn tyr)'%(self.range.get()*8)) cmd.select('lys7', 'name nz and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('lys8', 'name ce and resn lys within %s of (name od1 and resn asp)'%(self.range.get()*5.5)) cmd.select('lys9', 'name cg and resn lys within %s of (name ca and resn asp)'%(self.range.get()*9)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8 and byres lys9') cmd.select('his1', 'name cg and resn his within %s of (name cd and resn lys)'%(self.range.get()*6)) cmd.select('his2', 'name ne2 and resn his within %s of (name ce and resn lys)'%(self.range.get()*8)) cmd.select('his3', 'name nd1 and resn his within %s of (name cd and resn lys)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his5', 'name ce1 and resn his within %s of (name cz and resn tyr)'%(self.range.get()*6)) cmd.select('his6', 'name nd1 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*10.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name cg and resn asp)'%(self.range.get()*10)) cmd.select('his9', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('tyr1', 'name oh and resn tyr within %s of (name nz and resn lys )'%(self.range.get()*5)) cmd.select('tyr2', 'name ce2 and resn tyr within %s of (name nz and resn lys )'%(self.range.get()*6)) cmd.select('tyr3', 'name cz and resn tyr within %s of (name cg and resn lys)'%(self.range.get()*8)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr5', 'name cz and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*6)) cmd.select('tyr6', 'name ce1 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*7)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*7)) cmd.select('tyr8', 'name cz and resn tyr within %s of (name cb and resn asp)'%(self.range.get()*9)) cmd.select('tyr9', 'name ce2 and resn tyr within %s of (name ca and resn asp)'%(self.range.get()*8)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9') cmd.select('asp1', 'name od1 and resn asp within %s of (name nz and resn lys)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name ce and resn lys)'%(self.range.get()*5.5)) cmd.select('asp3', 'name ca and resn asp within %s of (name cg and resn lys)'%(self.range.get()*9)) cmd.select('asp4', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*10.5)) cmd.select('asp5', 'name cg and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*10)) cmd.select('asp6', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*9)) cmd.select('asp7', 'name od2 and resn asp within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('asp8', 'name cb and resn asp within %s of (name cz and resn tyr)'%(self.range.get()*9)) cmd.select('asp9', 'name ca and resn asp within %s of (name ce2 and resn tyr)'%(self.range.get()*8)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('aldoreductase', 'asp(his(lys(tyr)))') cmd.deselect() cmd.delete('lys') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys9') cmd.delete('lys1') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') def cistransisomerase2(self): self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*9)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name od1 and resn asp)'%(self.range.get()*11)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cg and resn asp)'%(self.range.get()*9.8)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name cb and resn asp)'%(self.range.get()*9.8)) cmd.select('tyr5', 'name cz and resn tyr within %s of (name od2 and resn asp)'%(self.range.get()*10.2)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name od1 and resn asp)'%(self.range.get()*11.5)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr8', 'name oh and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr9', 'name oh and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr10', 'name cz and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr11', 'name cz and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.8)) cmd.select('tyr12', 'name cz and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name cd1 and resn ile)'%(self.range.get()*6.3)) cmd.select('tyr14', 'name ce1 and resn tyr within %s of (name cg1 and resn ile)'%(self.range.get()*6.5)) cmd.select('tyr15', 'name ce1 and resn tyr within %s of (name cg2 and resn ile)'%(self.range.get()*5.5)) cmd.select('tyr', 'byres tyr1 and byre tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13 and byres tyr14 and byres tyr15') cmd.select('asp1', 'name od2 and resn asp within %s of (name oh and tyr)'%(self.range.get()*8.7)) cmd.select('asp2', 'name od1 and resn asp within %s of (name oh and tyr)'%(self.range.get()*10.5)) cmd.select('asp3', 'name cg and resn asp within %s of (name oh and tyr)'%(self.range.get()*9.3)) cmd.select('asp4', 'name cb and resn asp within %s of (name oh and tyr)'%(self.range.get()*9.3)) cmd.select('asp5', 'name od2 and resn asp within %s of (name cz and tyr)'%(self.range.get()*10)) cmd.select('asp6', 'name od1 and resn asp within %s of (name cz and resn tyr)'%(self.range.get()*11.1)) cmd.select('asp7', 'name od2 and resn asp within %s of (name cg2 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp8', 'name od2 and resn asp within %s of (name cd1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp9', 'name od2 and resn asp within %s of (name cg1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp10', 'name cb and resn asp within %s of (name cd1 and resn ile)'%(self.range.get()*10.8)) cmd.select('asp11', 'name cb and resn asp within %s of (name cg2 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp12', 'name cb and resn asp within %s of (name cg1 and resn ile)'%(self.range.get()*11.1)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10 and byres asp11 and byres asp12') cmd.select('ile1', 'name cd1 and resn ile within %s of (name oh and tyr)'%(self.range.get()*6.5)) cmd.select('ile2', 'name cg1 and resn ile within %s of (name oh and tyr)'%(self.range.get()*6.5)) cmd.select('ile3', 'name cg2 and resn ile within %s of (name oh and tyr)'%(self.range.get()*5.5)) cmd.select('ile4', 'name cd1 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*6.5)) cmd.select('ile5', 'name cg1 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*6.8)) cmd.select('ile6', 'name cg2 and resn ile within %s of (name cz and resn tyr)'%(self.range.get()*5.5)) cmd.select('ile7', 'name cd1 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*6.3)) cmd.select('ile8', 'name cg1 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('ile9', 'name cg2 and resn ile within %s of (name ce1 and resn tyr)'%(self.range.get()*5.5)) cmd.select('ile10', 'name cg2 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile11', 'name cd1 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile12', 'name cg1 and resn ile within %s of (name od2 and asp)'%(self.range.get()*11.5)) cmd.select('ile13', 'name cd1 and resn ile within %s of (name cb and asp)'%(self.range.get()*11)) cmd.select('ile14', 'name cg2 and resn ile within %s of (name cb and resn asp)'%(self.range.get()*11.5)) cmd.select('ile15', 'name cg1 and resn ile within %s of (name cb and resn asp)'%(self.range.get()*11.5)) cmd.select('ile', 'byres ile1 and byres ile2 and byres ile3 and byres ile4 and byres ile5 and byres ile6 and byres ile7 and byres ile8 and byres ile9 and byres ile10 and byres ile11 and byres ile12 and byres ile13 and byres ile14 and byres ile15') cmd.select('Cis-trans', 'ile(asp(tyr))') cmd.deselect() cmd.orient('Cis-trans') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr2') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('tyr14') cmd.delete('tyr15') cmd.delete('tyr') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp11') cmd.delete('asp12') cmd.delete('asp') cmd.delete('ile1') cmd.delete('ile2') cmd.delete('ile3') cmd.delete('ile4') cmd.delete('ile5') cmd.delete('ile6') cmd.delete('ile7') cmd.delete('ile8') cmd.delete('ile9') cmd.delete('ile10') cmd.delete('ile11') cmd.delete('ile12') cmd.delete('ile13') cmd.delete('ile14') cmd.delete('ile15') cmd.delete('ile') def nadhbinder22(self): self.deletemotif() cmd.select('asp1', 'name od2 and resn asp within %s of (name sg and resn cys)'%(self.range.get()*5)) cmd.select('asp2', 'name od2 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name sg and resn cys)'%(self.range.get()*6.4)) cmd.select('asp4', 'name od1 and resn asp within %s of (name cb and resn cys)'%(self.range.get()*7.2)) cmd.select('asp5', 'name cg and resn asp within %s of (name sg and resn cys)'%(self.range.get()*5.5)) cmd.select('asp6', 'name od2 and resn asp within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('asp7', 'name od2 and resn asp within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('asp8', 'name od1 and resn asp within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('asp9', 'name od1 and resn asp within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('asp10', 'name cg and resn asp within %s of (name og and resn ser)'%(self.range.get()*5.3)) cmd.select('asp11', 'name cg and resn asp within %s of (name cb and resn ser)'%(self.range.get()*6.4)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10 and byres asp11') cmd.select('cys1', 'name sg and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*5)) cmd.select('cys2', 'name cb and resn cys within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('cys3', 'name sg and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*6.4)) cmd.select('cys4', 'name cb and resn cys within %s of (name od1 and resn asp)'%(self.range.get()*7.2)) cmd.select('cys5', 'name sg and resn cys within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('cys6', 'name sg and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.4)) cmd.select('cys7', 'name sg and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name og and resn ser)'%(self.range.get()*8)) cmd.select('cys9', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*8.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('ser4', 'name cb and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('ser5', 'name og and resn ser within %s of (name cg and resn asp)'%(self.range.get()*5.3)) cmd.select('ser6', 'name cb and resn ser within %s of (name cg and resn asp)'%(self.range.get()*6.4)) cmd.select('ser7', 'name og and resn ser within %s of (name sg and resn cys)'%(self.range.get()*6.4)) cmd.select('ser8', 'name cb and resn ser within %s of (name sg and resn cys)'%(self.range.get()*7)) cmd.select('ser9', 'name og and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8)) cmd.select('ser10', 'name cb and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10') cmd.select('NAD-reductase', 'ser(asp(cys))') cmd.deselect() cmd.orient('NAD-reductase') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp11') cmd.delete('asp') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.delete('cys') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser') def nadhbinder222(self): self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('glu2', 'name oe2 and resn glu within %s of (name cb and resn cys)'%(self.range.get()*5.5)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('glu4', 'name oe1 and resn glu within %s of (name cb and resn cys)'%(self.range.get()*7.2)) cmd.select('glu5', 'name cg and resn glu within %s of (name sg and resn cys)'%(self.range.get()*5.5)) cmd.select('glu6', 'name oe2 and resn glu within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('glu7', 'name oe2 and resn glu within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('glu8', 'name oe1 and resn glu within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('glu9', 'name oe1 and resn glu within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('glu10', 'name cg and resn glu within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('glu11', 'name cg and resn glu within %s of (name cb and resn ser)'%(self.range.get()*6.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9 and byres glu10 and byres glu11') cmd.select('cys1', 'name sg and resn cys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys2', 'name cb and resn cys within %s of (name oe2 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys3', 'name sg and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*6.5)) cmd.select('cys4', 'name cb and resn cys within %s of (name oe1 and resn glu)'%(self.range.get()*7.5)) cmd.select('cys5', 'name sg and resn cys within %s of (name cg and resn glu)'%(self.range.get()*5.5)) cmd.select('cys6', 'name sg and resn cys within %s of (name og and resn ser)'%(self.range.get()*6.5)) cmd.select('cys7', 'name sg and resn cys within %s of (name cb and resn ser)'%(self.range.get()*7)) cmd.select('cys8', 'name cb and resn cys within %s of (name og and resn ser)'%(self.range.get()*8)) cmd.select('cys9', 'name cb and resn cys within %s of (name cb and resn ser)'%(self.range.get()*8.5)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('ser1', 'name og and resn ser within %s of (name oe2 and resn glu)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name oe2 and resn glu)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name oe1 and resn glu)'%(self.range.get()*6)) cmd.select('ser4', 'name cb and resn ser within %s of (name oe1 and resn glu)'%(self.range.get()*7)) cmd.select('ser5', 'name og and resn ser within %s of (name cg and resn glu)'%(self.range.get()*5.5)) cmd.select('ser6', 'name cb and resn ser within %s of (name cg and resn glu)'%(self.range.get()*6.5)) cmd.select('ser7', 'name og and resn ser within %s of (name sg and resn cys)'%(self.range.get()*6.5)) cmd.select('ser8', 'name cb and resn ser within %s of (name sg and resn cys)'%(self.range.get()*7)) cmd.select('ser9', 'name og and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8)) cmd.select('ser10', 'name cb and resn ser within %s of (name cb and resn cys)'%(self.range.get()*8.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9 and byres ser10') cmd.select('NAD-reductase2', 'ser(glu(cys))') cmd.deselect() cmd.orient('NAD-reductase2') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu10') cmd.delete('glu11') cmd.delete('glu') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') cmd.delete('cys') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser10') cmd.delete('ser') def cephdeacetylase2(self): self.deletemotif() cmd.select('his1', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*4.5)) cmd.select('his2', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5)) cmd.select('his3', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('his4', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his5', 'name ce1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('his6', 'name ne2 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*7)) cmd.select('his7', 'name ne2 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*6.5)) cmd.select('his8', 'name ne2 and resn his within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('his9', 'name ce1 and resn his within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('his10', 'name nd1 and resn his within %s of (name cb and resn ala)'%(self.range.get()*6.5)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('asp1', 'name od2 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8.5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9.5)) cmd.select('asp3', 'name cg and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9.5)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*4.5)) cmd.select('asp5', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5)) cmd.select('asp6', 'name cg and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp7', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp8', 'name od1 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*6)) cmd.select('asp9', 'name od1 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asp10', 'name od2 and resn asp within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9 and byres asp10') cmd.select('ala1', 'name cb and resn ala within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('ala2', 'name cb and resn ala within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('ala3', 'name cb and resn ala within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('ala4', 'name cb and resn ala within %s of (name od2 and resn asp)'%(self.range.get()*8.5)) cmd.select('ala5', 'name cb and resn ala within %s of (name od1 and resn asp)'%(self.range.get()*9.5)) cmd.select('ala6', 'name cb and resn ala within %s of (name cg and resn asp)'%(self.range.get()*9.5)) cmd.select('ala7', 'name c and resn ala within %s of (name n and resn gln)'%(self.range.get()*2.5)) cmd.select('ala', 'byres ala1 and byres ala2 and byres ala3 and byres ala4 and byres ala5 and byres ala6 and byres ala7') cmd.select('gln1', 'byres resn gln within %s of his'%(self.range.get()*9.5)) cmd.select('gln2', 'byres resn gln within %s of asp'%(self.range.get()*13.5)) cmd.select('gln3', 'byres resn gln within %s of ala'%(self.range.get()*3)) cmd.select('gln', 'byres gln1 and byres gln2 and byres gln3') cmd.select('deacetylase', 'his(asp(ala(gln)))') cmd.deselect() cmd.orient('deacetylase') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp') cmd.delete('ala1') cmd.delete('ala2') cmd.delete('ala3') cmd.delete('ala4') cmd.delete('ala5') cmd.delete('ala6') cmd.delete('ala7') cmd.delete('ala') cmd.delete('gln1') cmd.delete('gln2') cmd.delete('gln3') cmd.delete('gln') #hyaluronate/chondroitin lyase def chondrolyase2(self): self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name nh2 and resn arg)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne and resn arg)'%(self.range.get()*7)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*5)) cmd.select('tyr6', 'name oh and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*5)) cmd.select('tyr8', 'name ce2 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr9', 'name ce1 and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr12', 'name ce1 and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13') cmd.select('his1', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his2', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his3', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8)) cmd.select('his5', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his6', 'name nd1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his7', 'name ce1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('his9', 'name ne2 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('his10', 'name ne2 and resn his within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('his11', 'name ce1 and resn his within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('his12', 'name nd1 and resn his within %s of (name nh1 and resn arg)'%(self.range.get()*6.5)) cmd.select('his13', 'name nd1 and resn his within %s of (name cd and resn arg)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13') cmd.select('arg1', 'name nh2 and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg2', 'name nh1 and resn arg within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('arg3', 'name cz and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg4', 'name ne and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('arg6', 'name cz and resn arg within %s of (name ce1 and resn his)'%(self.range.get()*7)) cmd.select('arg7', 'name nh1 and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('arg8', 'name cd and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*9)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('arg10', 'name cz and resn arg within %s of (name cg and resn asn)'%(self.range.get()*12)) cmd.select('arg11', 'name nh2 and resn arg within %s of (name nd2 and resn asn)'%(self.range.get()*11.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byre arg11') cmd.select('asn1', 'name od1 and resn asn within %s of (name nh1 and resn arg)'%(self.range.get()*11)) cmd.select('asn2', 'name cg and resn asn within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('asn3', 'name nd2 and resn asn within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn6', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asn7', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn8', 'name od1 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn10', 'name od1 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11') cmd.select('chondroitinase', 'asn(his(arg(tyr)))') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg') def hyaluronlyase2(self): self.deletemotif() cmd.select('tyr1', 'name oh and resn tyr within %s of (name nh2 and resn arg)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('tyr4', 'name oh and resn tyr within %s of (name ne and resn arg)'%(self.range.get()*7)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*5)) cmd.select('tyr6', 'name oh and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr7', 'name oh and resn tyr within %s of (name ce1 and resn his)'%(self.range.get()*5)) cmd.select('tyr8', 'name ce2 and resn tyr within %s of (name nd1 and resn his)'%(self.range.get()*6)) cmd.select('tyr9', 'name ce1 and resn tyr within %s of (name ne2 and resn his)'%(self.range.get()*6)) cmd.select('tyr10', 'name oh and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr11', 'name oh and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*7.5)) cmd.select('tyr12', 'name ce1 and resn tyr within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('tyr13', 'name ce1 and resn tyr within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7 and byres tyr8 and byres tyr9 and byres tyr10 and byres tyr11 and byres tyr12 and byres tyr13') cmd.select('his1', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his2', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*8)) cmd.select('his3', 'name cd2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*7)) cmd.select('his4', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*8)) cmd.select('his5', 'name ne2 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his6', 'name nd1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('his7', 'name ce1 and resn his within %s of (name oh and resn tyr)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name ce2 and resn tyr)'%(self.range.get()*6)) cmd.select('his9', 'name ne2 and resn his within %s of (name ce1 and resn tyr)'%(self.range.get()*6)) cmd.select('his10', 'name ne2 and resn his within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('his11', 'name ce1 and resn his within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('his12', 'name nd1 and resn his within %s of (name nh1 and resn arg)'%(self.range.get()*6.5)) cmd.select('his13', 'name nd1 and resn his within %s of (name cd and resn arg)'%(self.range.get()*9)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10 and byres his11 and byres his12 and byres his13') cmd.select('arg1', 'name nh2 and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg2', 'name nh1 and resn arg within %s of (name oh and tyr)'%(self.range.get()*6)) cmd.select('arg3', 'name cz and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('arg4', 'name ne and resn arg within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('arg6', 'name cz and resn arg within %s of (name ce1 and resn his)'%(self.range.get()*7)) cmd.select('arg7', 'name nh1 and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('arg8', 'name cd and resn arg within %s of (name nd1 and resn his)'%(self.range.get()*9)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name od1 and resn asn)'%(self.range.get()*11)) cmd.select('arg10', 'name cz and resn arg within %s of (name cg and resn asn)'%(self.range.get()*12)) cmd.select('arg11', 'name nh2 and resn arg within %s of (name nd2 and resn asn)'%(self.range.get()*11.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10 and byre arg11') cmd.select('asn1', 'name od1 and resn asn within %s of (name nh1 and resn arg)'%(self.range.get()*11)) cmd.select('asn2', 'name cg and resn asn within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('asn3', 'name nd2 and resn asn within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('asn4', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*7)) cmd.select('asn5', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn6', 'name od1 and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*7)) cmd.select('asn7', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*8)) cmd.select('asn8', 'name od1 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn9', 'name nd2 and resn asn within %s of (name oh and resn tyr)'%(self.range.get()*7.5)) cmd.select('asn10', 'name od1 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn11', 'name nd2 and resn asn within %s of (name ce1 and resn tyr)'%(self.range.get()*6.5)) cmd.select('asn', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8 and byres asn9 and byres asn10 and byres asn11') cmd.select('Hyaluronate_Lyase', 'asn(his(arg(tyr)))') cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('tyr') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('tyr10') cmd.delete('tyr11') cmd.delete('tyr12') cmd.delete('tyr13') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr8') cmd.delete('tyr9') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg11') cmd.delete('arg') def ACTase2(self): self.deletemotif() cmd.select('gln', 'resi 231 and resn gln') cmd.select('arg', 'resi 167 and resn arg(resi 229 and resn arg)') cmd.select('thr', 'resi 55 and resn thr(resi 53 and resn thr)') cmd.select('his', 'resi 134 and resn his') cmd.select('lys', 'resi 84 and resn lys') cmd.select('ser', 'resi 80 and resn ser') cmd.select('actase', 'gln(arg(thr(his(lys(ser)))))') cmd.delete('arg') cmd.delete('lys') cmd.delete('thr') cmd.delete('ser') cmd.delete('gln') cmd.delete('his') def exonucleaseiii2(self): self.deletemotif() cmd.select('his1', 'name ne2 and resn his within %s of (name nd2 and resn asn)'%(self.range.get()*5.5)) cmd.select('his2', 'name ne2 and resn his within %s of (name od1 and resn asn)'%(self.range.get()*6.5)) cmd.select('his3', 'name ne2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*5.5)) cmd.select('his4', 'name cd2 and resn his within %s of (name cg and resn asn)'%(self.range.get()*5.5)) cmd.select('his5', 'name nd1 and resn his within %s of (name cg and resn asn)'%(self.range.get()*6.5)) cmd.select('his6', 'name ce1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his7', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5)) cmd.select('his8', 'name nd1 and resn his within %s of (name od1 and resn asp)'%(self.range.get()*5.5)) cmd.select('his9', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('asp1', 'name od2 and resn asp within %s of (name ce1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp2', 'name od2 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp4', 'name cg and resn asp within %s of (name nd1 and resn his)'%(self.range.get()*5.5)) cmd.select('asp5', 'name od2 and resn asp within %s of (name nd2 and resn asn)'%(self.range.get()*5.7)) cmd.select('asp6', 'name od1 and resn asp within %s of (name nd2 and resn asn)'%(self.range.get()*6)) cmd.select('asp7', 'name od1 and resn asp within %s of (name od1 and resn asn)'%(self.range.get()*6)) cmd.select('asp8', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7') cmd.select('asp9', 'byres resn asp within %s of asp8'%(self.range.get()*5.5)) cmd.select('asp10', 'byres resn asp within %s of his'%(self.range.get()*5.5)) cmd.select('asp', 'byres asp8 or (byres asp9 and byres asp10)') cmd.select('asn1', 'name nd2 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn2', 'name od1 and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*6.5)) cmd.select('asn3', 'name cg and resn asn within %s of (name ne2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn4', 'name cg and resn asn within %s of (name cd2 and resn his)'%(self.range.get()*5.5)) cmd.select('asn5', 'name cg and resn asn within %s of (name nd1 and resn his)'%(self.range.get()*6.5)) cmd.select('asn6', 'name nd2 and resn asn within %s of (name od2 and resn asp)'%(self.range.get()*5.7)) cmd.select('asn7', 'name nd2 and resn asn within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('asn8', 'name od1 and resn asn within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('asn9', 'byres asn1 and byres asn2 and byres asn3 and byres asn4 and byres asn5 and byres asn6 and byres asn7 and byres asn8') cmd.select('asn10', 'byres resn asn within %s of asn9'%(self.range.get()*8)) cmd.select('asn11', 'byres resn asn within %s of his'%(self.range.get()*8)) cmd.select('asn12', 'byres resn asn within %s of asp8'%(self.range.get()*6)) cmd.select('asn', 'byres asn9 or (byres asn10 and byres asn11 and byres asn12)') cmd.select('Exonuclease3', 'his(asp(asn))') cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his') cmd.delete('asn1') cmd.delete('asn2') cmd.delete('asn3') cmd.delete('asn4') cmd.delete('asn5') cmd.delete('asn6') cmd.delete('asn7') cmd.delete('asn8') cmd.delete('asn9') cmd.delete('asn10') cmd.delete('asn11') cmd.delete('asn12') cmd.delete('asn') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp10') cmd.delete('asp') def adenylatekinase2(self): self.deletemotif() #p-loop first cmd.select('lys1', 'name nz and resn lys within %s of (name n and resn gly)'%(self.range.get()*7.5)) cmd.select('lys2', 'name cg and resn lys within %s of (name c and resn gly)'%(self.range.get()*6)) cmd.select('lys3', 'name n and resn lys within %s of (name n and resn gly)'%(self.range.get()*5)) cmd.select('lys4', 'name n and resn lys within %s of (resn gly)'%(self.range.get()*2)) cmd.select('lys5', 'name c and resn lys within %s of (resn gly)'%(self.range.get()*2)) cmd.select('lys6', 'name nz and resn lys within %s of (name od2 and resn asp)'%(self.range.get()*13)) cmd.select('lys7', 'name nz and resn lys within %s of (name ne and resn arg)'%(self.range.get()*11)) cmd.select('lys8', 'name nz and resn lys within %s of (name nh2 and resn arg)'%(self.range.get()*9.5)) cmd.select('lys', 'byres lys1 and byres lys2 and byres lys3 and byres lys4 and byres lys5 and byres lys6 and byres lys7 and byres lys8') cmd.select('glya1', 'name n and resn gly within %s of (name nz and lys)'%(self.range.get()*7.5)) cmd.select('glya2', 'name ca and resn gly within %s of (name cg and lys)'%(self.range.get()*7)) cmd.select('glya3', 'name c and resn gly within %s of (name n and lys)'%(self.range.get()*2)) cmd.select('glya4', 'name n and resn gly within %s of (name nh1 and resn arg)'%(self.range.get()*10)) cmd.select('glya', 'byres glya1 and byres glya2 and byres glya3 and byres glya4') cmd.select('glyb', 'name n and resn gly within %s of (name c and lys)'%(self.range.get()*2)) cmd.select('p-loop', 'lys(glya(byres glyb))') cmd.select('asp1', 'name od2 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('asp2', 'name od1 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('asp3', 'name od1 and resn asp within %s of (name nh1 and resn arg)'%(self.range.get()*5)) cmd.select('asp4', 'name od2 and resn asp within %s of p-loop'%(self.range.get()*15)) cmd.select('aspa', 'byres asp1 and byres asp2 and byres asp3 and byres asp4') cmd.select('aspb1', 'name od2 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('aspb2', 'name cg and resn asp within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('aspb3', 'name od1 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('aspb4', 'name od2 and resn asp within %s of (name od1 and aspa)'%(self.range.get()*7)) cmd.select('aspb5', 'name cg and resn asp within %s of (name cg and aspa)'%(self.range.get()*7)) cmd.select('aspb6', 'name od1 and resn asp within %s of (name od2 and aspa)'%(self.range.get()*7)) cmd.select('asp', 'byres aspb1 and byres aspb2 and byres aspb3 and byres aspb4 and byres aspb5 and byres aspb6') cmd.select('arg1', 'name nh1 and resn arg within %s of (name od1 and asp or name od2 and asp)'%(self.range.get()*4.9)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name od1 and asp or name od2 and asp)'%(self.range.get()*4.9)) cmd.select('arg', 'byres arg1 or byres arg2') cmd.select('adenylatekinase', 'p-loop(asp(aspa(arg)))') cmd.deselect() cmd.delete('lys1') cmd.delete('lys2') cmd.delete('lys3') cmd.delete('lys4') cmd.delete('lys5') cmd.delete('lys6') cmd.delete('lys7') cmd.delete('lys8') cmd.delete('lys') cmd.delete('glya1') cmd.delete('glya2') cmd.delete('glya3') cmd.delete('glya4') cmd.delete('glya') cmd.delete('glyb') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('aspa') cmd.delete('aspb1') cmd.delete('aspb2') cmd.delete('aspb3') cmd.delete('aspb4') cmd.delete('aspb5') cmd.delete('aspb6') cmd.delete('asp') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg') def citratesynth2(self): self.deletemotif() cmd.select('his1', 'name ne2 and resn his within %s of (name og and resn ser)'%(self.range.get()*5)) cmd.select('his2', 'name ne2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('his3', 'name ce1 and resn his within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('his4', 'name ce1 and resn his within %s of (name cb and resn ser)'%(self.range.get()*6.5)) cmd.select('his5', 'name cd2 and resn his within %s of (name og and resn ser)'%(self.range.get()*6)) cmd.select('his6', 'name nd1 and resn his within %s of (name og and resn ser)'%(self.range.get()*7)) cmd.select('his7', 'name nd1 and resn his within %s of (name od2 and resn asp)'%(self.range.get()*8)) cmd.select('his8', 'name nd1 and resn his within %s of (name cg and resn asp)'%(self.range.get()*8.5)) cmd.select('his9', 'name o and resn his within %s of (name od2 and resn asp)'%(self.range.get()*5.5)) cmd.select('his10', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9') cmd.select('his11', 'byres resn his within %s of his10'%(self.range.get()*8.2)) cmd.select('ser1', 'name og and resn ser within %s of (name ne2 and his10)'%(self.range.get()*5)) cmd.select('ser2', 'name cb and resn ser within %s of (name ne2 and his10)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name ce1 and his10)'%(self.range.get()*5.5)) cmd.select('ser4', 'name cb and resn ser within %s of (name ce1 and his10)'%(self.range.get()*6.5)) cmd.select('ser5', 'name og and resn ser within %s of (name cd2 and his10)'%(self.range.get()*6)) cmd.select('ser6', 'name og and resn ser within %s of (name nd1 and his10)'%(self.range.get()*7)) cmd.select('ser7', 'name og and resn ser within %s of (name od2 and resn asp)'%(self.range.get()*12)) cmd.select('ser8', 'name og and resn ser within %s of (name cg and resn asp)'%(self.range.get()*12)) cmd.select('ser9', 'name og and resn ser within %s of (name od1 and resn asp)'%(self.range.get()*12)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('his12', 'byres resn his within %s of ser'%(self.range.get()*12)) cmd.select('asp1', 'name od2 and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp2', 'name cg and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp3', 'name od1 and resn asp within %s of (name og and ser)'%(self.range.get()*12)) cmd.select('asp4', 'name od2 and resn asp within %s of (name nd1 and his10)'%(self.range.get()*8)) cmd.select('asp5', 'name cg and resn asp within %s of (name nd1 and his10)'%(self.range.get()*8.5)) cmd.select('asp6', 'name od2 and resn asp within %s of (name o and his10)'%(self.range.get()*5.5)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6') cmd.select('his13', 'byres resn his within %s of asp'%(self.range.get()*8.5)) cmd.select('his', 'byres his10 or (byres his11 and byres his12 and byres his13)') cmd.select('Citrate_Synth', 'his(asp(ser))') cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his11') cmd.delete('his12') cmd.delete('his13') cmd.delete('his') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp') def tyrosinekinase2(self): self.deletemotif() cmd.select('arg1', 'name nh1 and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5)) cmd.select('arg2', 'name nh2 and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('arg3', 'name cz and resn arg within %s of (name cb and resn ala)'%(self.range.get()*5.5)) cmd.select('arg4', 'name ne and resn arg within %s of (name cb and resn ala)'%(self.range.get()*6)) cmd.select('arg5', 'name nh2 and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg6', 'name nh2 and resn arg within %s of (name cg and resn asp)'%(self.range.get()*5.5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name od2 and resn asp)'%(self.range.get()*6)) cmd.select('arg8', 'name cz and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg9', 'name ne and resn arg within %s of (name od1 and resn asp)'%(self.range.get()*6)) cmd.select('arg10', 'name ne and resn arg within %s of (name cg and resn asp)'%(self.range.get()*6.5)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9 and byres arg10') cmd.select('asp1', 'name od1 and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5.5)) cmd.select('asp2', 'name cg and resn asp within %s of (name nh2 and resn arg)'%(self.range.get()*5.5)) cmd.select('asp3', 'name od2 and resn asp within %s of (name nh2 and arg)'%(self.range.get()*7)) cmd.select('asp4', 'name od1 and resn asp within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('asp5', 'name od1 and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6)) cmd.select('asp6', 'name cg and resn asp within %s of (name ne and resn arg)'%(self.range.get()*6.5)) cmd.select('asp7', 'name od1 and resn asp within %s of (name cb and resn ala)'%(self.range.get()*9)) cmd.select('asp8', 'name o and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8)) cmd.select('asp9', 'name cg and resn asp within %s of (name cb and resn ala)'%(self.range.get()*8)) cmd.select('asp', 'byres asp1 and byres asp2 and byres asp3 and byres asp4 and byres asp5 and byres asp6 and byres asp7 and byres asp8 and byres asp9') cmd.select('ala1', 'name cb and resn ala within %s of (name nh1 and arg)'%(self.range.get()*5)) cmd.select('ala2', 'name cb and resn ala within %s of (name nh2 and arg)'%(self.range.get()*5.5)) cmd.select('ala3', 'name cb and resn ala within %s of (name cz and arg)'%(self.range.get()*5.5)) cmd.select('ala4', 'name cb and resn ala within %s of (name ne and arg)'%(self.range.get()*6)) cmd.select('ala5', 'name cb and resn ala within %s of (name od1 and asp)'%(self.range.get()*9)) cmd.select('ala6', 'name cb and resn ala within %s of (name o and asp)'%(self.range.get()*8)) cmd.select('ala7', 'name cb and resn ala within %s of (name cg and asp)'%(self.range.get()*8)) cmd.select('ala', 'byres ala1 and byres ala2 and byres ala3 and byres ala4 and byres ala5 and byres ala6 and byres ala7') cmd.select('SRC-Kinase', 'ala(asp(arg))') cmd.deselect() cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg10') cmd.delete('arg') cmd.delete('asp1') cmd.delete('asp2') cmd.delete('asp3') cmd.delete('asp4') cmd.delete('asp5') cmd.delete('asp6') cmd.delete('asp7') cmd.delete('asp8') cmd.delete('asp9') cmd.delete('asp') cmd.delete('ala1') cmd.delete('ala2') cmd.delete('ala3') cmd.delete('ala4') cmd.delete('ala5') cmd.delete('ala6') cmd.delete('ala7') cmd.delete('ala') def hhal2(self): self.deletemotif() cmd.select('glu1', 'name oe2 and resn glu within %s of (name sg and resn cys)'%(self.range.get()*10)) cmd.select('glu2', 'name cd and resn glu within %s of (name cb and resn cys)'%(self.range.get()*10)) cmd.select('glu3', 'name oe1 and resn glu within %s of (name ca and resn cys)'%(self.range.get()*10)) cmd.select('glu4', 'name oe2 and resn glu within %s of (name ne and resn arg)'%(self.range.get()*5)) cmd.select('glu5', 'name cd and resn glu within %s of (name cz and resn arg)'%(self.range.get()*6)) cmd.select('glu6', 'name oe1 and resn glu within %s of (name nh2 and resn arg)'%(self.range.get()*5)) cmd.select('glu7', 'name cg and resn glu within %s of (name ca and resn phe)'%(self.range.get()*10)) cmd.select('glu8', 'name cd and resn glu within %s of (name cb and resn phe)'%(self.range.get()*10)) cmd.select('glu9', 'name ca and resn glu within %s of (name cd1 and resn phe)'%(self.range.get()*7.5)) cmd.select('glu', 'byres glu1 and byres glu2 and byres glu3 and byres glu4 and byres glu5 and byres glu6 and byres glu7 and byres glu8 and byres glu9') cmd.select('cys1', 'name sg and resn cys within %s of (name nh1 and resn arg)'%(self.range.get()*6)) cmd.select('cys2', 'name cb and resn cys within %s of (name cz and resn arg)'%(self.range.get()*7)) cmd.select('cys3', 'name ca and resn cys within %s of (name nh2 and resn arg)'%(self.range.get()*8)) cmd.select('cys4', 'name sg and resn cys within %s of (name oe2 and glu)'%(self.range.get()*10)) cmd.select('cys5', 'name cb and resn cys within %s of (name cd and glu)'%(self.range.get()*10)) cmd.select('cys6', 'name ca and resn cys within %s of (name oe1 and glu)'%(self.range.get()*10)) cmd.select('cys7', 'name ca and resn cys within %s of (name ca and resn phe)'%(self.range.get()*8.5)) cmd.select('cys8', 'name cb and resn cys within %s of (name cd2 and resn phe)'%(self.range.get()*9)) cmd.select('cys9', 'name sg and resn cys within %s of (name cd1 and resn phe)'%(self.range.get()*12)) cmd.select('cys', 'byres cys1 and byres cys2 and byres cys3 and byres cys4 and byres cys5 and byres cys6 and byres cys7 and byres cys8 and byres cys9') cmd.select('arg1', 'name nh1 and resn arg within %s of (name sg and resn cys)'%(self.range.get()*6)) cmd.select('arg2', 'name cz and resn arg within %s of (name cb and resn cys)'%(self.range.get()*7)) cmd.select('arg3', 'name nh2 and resn arg within %s of (name ca and resn cys)'%(self.range.get()*8)) cmd.select('arg4', 'name ne and resn arg within %s of (name oe2 and glu)'%(self.range.get()*5)) cmd.select('arg5', 'name cz and resn arg within %s of (name cd and glu)'%(self.range.get()*6)) cmd.select('arg6', 'name nh2 and resn arg within %s of (name oe1 and glu)'%(self.range.get()*5)) cmd.select('arg7', 'name nh2 and resn arg within %s of (name ce1 and resn phe)'%(self.range.get()*10.5)) cmd.select('arg8', 'name cz and resn arg within %s of (name cz and resn phe)'%(self.range.get()*11.5)) cmd.select('arg9', 'name nh1 and resn arg within %s of (name ce2 and resn phe)'%(self.range.get()*12)) cmd.select('arg', 'byres arg1 and byres arg2 and byres arg3 and byres arg4 and byres arg5 and byres arg6 and byres arg7 and byres arg8 and byres arg9') cmd.select('phe1', 'name ca and resn phe within %s of (name cg and glu)'%(self.range.get()*10)) cmd.select('phe2', 'name cb and resn phe within %s of (name cb and glu)'%(self.range.get()*10)) cmd.select('phe3', 'name cd1 and resn phe within %s of (name ca and glu)'%(self.range.get()*7.5)) cmd.select('phe4', 'name ce1 and resn phe within %s of (name nh2 and resn arg)'%(self.range.get()*10.5)) cmd.select('phe5', 'name cz and resn phe within %s of (name cz and resn arg)'%(self.range.get()*11.5)) cmd.select('phe6', 'name ce2 and resn phe within %s of (name nh1 and resn arg)'%(self.range.get()*12)) cmd.select('phe7', 'name ca and resn phe within %s of (name ca and cys)'%(self.range.get()*8.5)) cmd.select('phe8', 'name cd2 and resn phe within %s of (name cb and cys)'%(self.range.get()*9)) cmd.select('phe9', 'name cd1 and resn phe within %s of (name sg and cys)'%(self.range.get()*12)) cmd.select('phe', 'byres phe1 and byres phe2 and byres phe3 and byres phe4 and byres phe5 and byres phe6 and byres phe7 and byres phe8 and byres phe9') cmd.select('hhal', 'glu(arg(phe(cys)))') cmd.deselect() cmd.orient('hhal') cmd.delete('arg1') cmd.delete('arg2') cmd.delete('arg3') cmd.delete('arg4') cmd.delete('arg5') cmd.delete('arg6') cmd.delete('arg7') cmd.delete('arg8') cmd.delete('arg9') cmd.delete('arg') cmd.delete('glu1') cmd.delete('glu2') cmd.delete('glu3') cmd.delete('glu4') cmd.delete('glu5') cmd.delete('glu6') cmd.delete('glu7') cmd.delete('glu8') cmd.delete('glu9') cmd.delete('glu') cmd.delete('phe') cmd.delete('phe1') cmd.delete('phe2') cmd.delete('phe3') cmd.delete('phe4') cmd.delete('phe5') cmd.delete('phe6') cmd.delete('phe7') cmd.delete('phe8') cmd.delete('phe9') cmd.delete('cys') cmd.delete('cys1') cmd.delete('cys2') cmd.delete('cys3') cmd.delete('cys4') cmd.delete('cys5') cmd.delete('cys6') cmd.delete('cys7') cmd.delete('cys8') cmd.delete('cys9') def serotoninacetyl2(self): cmd.select('his1', 'name ne2 and resn his within %s of (name og and resn ser)'%(self.range.get()*4.5)) cmd.select('his2', 'name ne2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*5.5)) cmd.select('his3', 'name cd2 and resn his within %s of (name og and resn ser)'%(self.range.get()*5.5)) cmd.select('his4', 'name cd2 and resn his within %s of (name cb and resn ser)'%(self.range.get()*6)) cmd.select('his5', 'name ne2 and resn his within %s of (name o and resn leu)'%(self.range.get()*6)) cmd.select('his6', 'name ce1 and resn his within %s of (name cd1 and resn leu)'%(self.range.get()*10)) cmd.select('his7', 'name ce1 and resn his within %s of (name cb and resn leu)'%(self.range.get()*9)) cmd.select('his8', 'name nd1 and resn his within %s of (name og and resn ser)'%(self.range.get()*7.5)) cmd.select('his9', 'name o and resn his within %s of (name oh and resn tyr)'%(self.range.get()*10)) cmd.select('his10', 'name cb and resn his within %s of (name oh and resn tyr)'%(self.range.get()*12)) cmd.select('his', 'byres his1 and byres his2 and byres his3 and byres his4 and byres his5 and byres his6 and byres his7 and byres his8 and byres his9 and byres his10') cmd.select('ser1', 'name og and resn ser within %s of (name ne2 and his)'%(self.range.get()*4.5)) cmd.select('ser2', 'name cb and resn ser within %s of (name ne2 and his)'%(self.range.get()*5.5)) cmd.select('ser3', 'name og and resn ser within %s of (name cd2 and his)'%(self.range.get()*5.5)) cmd.select('ser4', 'name cb and resn ser within %s of (name cd2 and his)'%(self.range.get()*6)) cmd.select('ser5', 'name og and resn ser within %s of (name nd1 and his)'%(self.range.get()*7.5)) cmd.select('ser6', 'name og and resn ser within %s of (name o and resn leu)'%(self.range.get()*5)) cmd.select('ser7', 'name og and resn ser within %s of (name cb and resn leu)'%(self.range.get()*8)) cmd.select('ser8', 'name cb and resn ser within %s of (name o and resn leu)'%(self.range.get()*5.5)) cmd.select('ser9', 'name n and resn ser within %s of (name cd2 and his)'%(self.range.get()*5.5)) cmd.select('ser', 'byres ser1 and byres ser2 and byres ser3 and byres ser4 and byres ser5 and byres ser6 and byres ser7 and byres ser8 and byres ser9') cmd.select('leu1', 'name o and resn leu within %s of (name ne2 and his)'%(self.range.get()*6)) cmd.select('leu2', 'name cd1 and resn leu within %s of (name ce1 and his)'%(self.range.get()*10)) cmd.select('leu3', 'name cb and resn leu within %s of (name ce1 and his)'%(self.range.get()*9)) cmd.select('leu4', 'name o and resn leu within %s of (name og and ser)'%(self.range.get()*5)) cmd.select('leu5', 'name cb and resn leu within %s of (name og and ser)'%(self.range.get()*8)) cmd.select('leu6', 'name o and resn leu within %s of (name cb and ser)'%(self.range.get()*5.5)) cmd.select('leu7', 'name n and resn leu within %s of (name ce1 and resn his)'%(self.range.get()*7.5)) cmd.select('leu8', 'byres leu1 and byres leu2 and byres leu3 and byres leu4 and byres leu5 and byres leu6 and byres leu7') cmd.select('leu9', 'name n and resn leu within %s of (name o and his)'%(self.range.get()*7)) cmd.select('leu10', 'name n and resn leu within %s of (name c and his)'%(self.range.get()*6.5)) cmd.select('leu11', 'name n and resn leu within %s of (name n and his)'%(self.range.get()*8)) cmd.select('leu12', 'name cd1 and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*6)) cmd.select('leu13', 'name cb and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*5.5)) cmd.select('leu14', 'name cg and resn leu within %s of (name oh and resn tyr)'%(self.range.get()*7)) cmd.select('leu15', 'name cd1 and resn leu within %s of (name cz and resn tyr)'%(self.range.get()*6.5)) cmd.select('leu15b', 'name cd1 and resn leu within %s of (name ce1 and resn tyr)'%(self.range.get()*5.5)) cmd.select('leu16', 'byres leu9 and byres leu15b and byres leu10 and byres leu11 and byres leu12 and byres leu13 and byres leu14 and byres leu15') cmd.select('tyr1', 'name oh and resn tyr within %s of (name cd1 and leu16)'%(self.range.get()*6)) cmd.select('tyr2', 'name oh and resn tyr within %s of (name cb and leu16)'%(self.range.get()*6.5)) cmd.select('tyr3', 'name oh and resn tyr within %s of (name cg and leu16)'%(self.range.get()*7)) cmd.select('tyr4', 'name cz and resn tyr within %s of (name cd1 and leu16)'%(self.range.get()*6.5)) cmd.select('tyr5', 'name oh and resn tyr within %s of (name n and his)'%(self.range.get()*10)) cmd.select('tyr6', 'name cz and resn tyr within %s of (name c and his)'%(self.range.get()*10.2)) cmd.select('tyr7', 'name ce1 and resn tyr within %s of (name o and ser)'%(self.range.get()*16)) cmd.select('tyr', 'byres tyr1 and byres tyr2 and byres tyr3 and byres tyr4 and byres tyr5 and byres tyr6 and byres tyr7') cmd.select('Serotonin_transferase', 'his(ser(leu8(leu16(tyr))))') cmd.deselect() cmd.delete('his1') cmd.delete('his2') cmd.delete('his3') cmd.delete('his4') cmd.delete('his5') cmd.delete('his6') cmd.delete('his7') cmd.delete('his8') cmd.delete('his9') cmd.delete('his10') cmd.delete('his') cmd.delete('ser1') cmd.delete('ser2') cmd.delete('ser3') cmd.delete('ser4') cmd.delete('ser5') cmd.delete('ser6') cmd.delete('ser7') cmd.delete('ser8') cmd.delete('ser9') cmd.delete('ser') cmd.delete('leu1') cmd.delete('leu2') cmd.delete('leu3') cmd.delete('leu4') cmd.delete('leu5') cmd.delete('leu6') cmd.delete('leu7') cmd.delete('leu8') cmd.delete('leu9') cmd.delete('leu10') cmd.delete('leu11') cmd.delete('leu12') cmd.delete('leu13') cmd.delete('leu14') cmd.delete('leu15') cmd.delete('leu15b') cmd.delete('leu16') cmd.delete('leu') cmd.delete('tyr1') cmd.delete('tyr2') cmd.delete('tyr3') cmd.delete('tyr4') cmd.delete('tyr5') cmd.delete('tyr6') cmd.delete('tyr7') cmd.delete('tyr') #motif options def motifoption(self, tag): if tag=='Surface Pocket': self.surfmotifer() elif tag=='Polar Contacts': self.motifcontact() elif tag=='Hide Contacts': self.hidecontact() elif tag=='Show Substrate': self.showsubstrate() elif tag=='Show label': self.labelmotif() elif tag=='Hide Label': self.dellabel() elif tag=='Hide Substrate': self.hidesubstrate() #Show binding pocket def surfmotifer(self): objects = cmd.get_names('all') cmd.set('transparency', '0.5', 'all') try: if 'Adjacent' in objects: if 'Peroxidase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Peroxidase and !Adjacent') if 'carboncarbon' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!carboncarbon and !Adjacent') if 'o-glycosyl' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!o-glycosyl and !Adjacent') if 'Tkinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Tkinase and !Adjacent') if 'Ligase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Ligase and !Adjacent') if 'glu_amidotransferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!glu_amidotransferase and !Adjacent') if 'fucoseisomerase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!fucoseisomerase and !Adjacent') if 'Aminotransferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Aminotransferase and !Adjacent') if 'Zinc_finger' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Zinc_finger and !Adjacent') if 'paplike' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!paplike and !Adjacent') if 'carbonicanhydrase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!carbonicanhydrase and !Adjacent') if 'tyrophos' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!tyrophos and !Adjacent') if 'metalloprotease' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!metalloprotease and !Adjacent') if 'superoxide' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!superoxide and !Adjacent') if 'lactamase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!lactamase and !Adjacent') if 'serineprotease' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!serineprotease and !Adjacent') if 'TrioseIsomerase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!TrioseIsomerase and !Adjacent') if 'alcoholdehyd' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!alcoholdehyd and !Adjacent') if 'aldoreductase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!aldoreductase and !Adjacent') if 'Cis-trans' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Cis-trans and !Adjacent') if 'NAD-reductase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!NAD-reductase and !Adjacent') if 'NAD-reductase2' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!NAD-reductase2 and !Adjacent') if 'deacetylase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!deacetylase and !Adjacent') if 'chondroitinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!chondroitinase and !Adjacent') if 'Hyaluronate_Lyase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Hyaluronate_Lyase and !Adjacent') if 'Cyclin_Kinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Cyclin_Kinase and !Adjacent') if 'SRC-Kinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!SRC-Kinase and !Adjacent') if 'Serotonin_transferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Serotonin_transferase and !Adjacent') if 'deacetylase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!deacetylase and !Adjacent') if 'adenylatekinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!adenylatekinase and !Adjacent') if 'actase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!actase and !Adjacent') if 'Exonuclease3' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Exonuclease3 and !Adjacent') if 'Citrate_Synth' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Citrate_Synth and !Adjacent') if 'hhal' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!hhal and !Adjacent') if 'Exonuclease3' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Exonuclease3 and !Adjacent') self.cpksubstrate() cmd.orient('all') else: if 'Peroxidase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Peroxidase') if 'carboncarbon' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!carboncarbon') if 'o-glycosyl' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!o-glycosyl') if 'Tkinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Tkinase') if 'Ligase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Ligase') if 'glu_amidotransferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!glu_amidotransferase') if 'fucoseisomerase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!fucoseisomerase') if 'Aminotransferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Aminotransferase') if 'Zinc_finger' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Zinc_finger') if 'paplike' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!paplike') if 'carbonicanhydrase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!carbonicanhydrase') if 'tyrophos' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!tyrophos') if 'metalloprotease' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!metalloprotease') if 'superoxide' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!superoxide') if 'lactamase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!lactamase') if 'serineprotease' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!serineprotease') if 'TrioseIsomerase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!TrioseIsomerase') if 'alcoholdehyd' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!alcoholdehyd') if 'aldoreductase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!aldoreductase') if 'Cis-trans' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Cis-trans') if 'NAD-reductase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!NAD-reductase') if 'NAD-reductase2' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!NAD-reductase2') if 'deacetylase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!deacetylase') if 'chondroitinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!chondroitinase') if 'Hyaluronate_Lyase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Hyaluronate_Lyase') if 'Cyclin_Kinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Cyclin_Kinase') if 'SRC-Kinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!SRC-Kinase') if 'Serotonin_transferase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Serotonin_transferase') if 'deacetylase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!deacetylase') if 'adenylatekinase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!adenylatekinase') if 'actase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!actase') if 'Exonuclease3' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Exonuclease3') if 'Citrate_Synth' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!Citrate_Synth') if 'hhal' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!hhal') if 'betaine_dehydrogenase' in objects: cmd.show('surface', 'all') cmd.hide('cartoon', 'all') cmd.color('white', '!betaine_dehydrogenase') self.cpksubstrate() cmd.orient('all') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select a motif') #polar contacts def motifcontact(self): objects = cmd.get_names('all') try: try: cmd.dist(self.mot+"_polar_conts",self.mot,self.mot,quiet=1,mode=2,label=0,reset=1) cmd.enable(self.mot+"_polar_conts") except: cmd.dist("motif_polar_conts","motif","motif",quiet=1,mode=2,label=0,reset=1) cmd.enable("motif_polar_conts") if 'Adjacent' in objects: cmd.dist('Adjacent_polar_conts','Adjacent','Adjacent',quiet=1,mode=2,label=0,reset=1) if 'substrate' in objects: cmd.dist(self.mot+"_around_polar_conts",self.mot,"(byobj ("+self.mot+")) and (not ("+self.mot+"))",quiet=1,mode=2,label=0,reset=1) cmd.enable(self.mot+"_around_polar_conts") except: import tkMessageBox tkMessageBox.showinfo('Alert', "Select a motif first") def hidecontact(self): objects = cmd.get_names('all') try: try: cmd.delete(self.mot+"_polar_conts") except: cmd.delete("motif_polar_conts") if 'Adjacent' in objects: cmd.delete('Adjacent_polar_conts') if 'substrate' in objects: cmd.delete(self.mot+"_around"+"_polar_conts") except: import tkMessageBox tkMessageBox.showinfo('Alert', "No motif polar contacts to hide") #develop spot #substrate# def showsubstrate(self): try: try: cmd.select('substrate', 'byres het within 7 of '+self.mot) objects = cmd.get_names('all') xp = cmd.index('substrate') np = len(xp) if(np < 1): cmd.delete('substrate') if 'substrate' in objects: cmd.show('sticks', 'substrate') cmd.deselect() self.cpksubstrate() except: cmd.select('substrate', 'byres het within 7 of motif') objects = cmd.get_names('all') xp = cmd.index('substrate') np = len(xp) if(np < 1): cmd.delete('substrate') if 'substrate' in objects: cmd.show('sticks', 'substrate') cmd.deselect() self.cpksubstrate() except: import tkMessageBox tkMessageBox.showinfo('Alert', "No substrate found") def hidesubstrate(self): try: cmd.hide('sticks', 'substrate') except: import tkMessageBox tkMessageBox.showinfo('Alert', "No substrate selected") #Labels def dellabel(self): objects = cmd.get_names('all') try: try: cmd.label(self.mot,"''") except: cmd.label("motif","''") if 'Adjacent' in objects: cmd.label('byres Adjacent',"''") except: import tkMessageBox tkMessageBox.showinfo('Alert', "No motif labels to hide") def labelmotif(self): objects = cmd.get_names('all') try: try: cmd.label('''(name ca+C1*+C1' and (byres('''+self.mot+''')))''','''"%s-%s"%(resn,resi)''') except: cmd.label('''(name ca+C1*+C1' and (byres(motif)))''','''"%s-%s"%(resn,resi)''') if 'Adjacent' in objects: cmd.label('''(name ca+C1*+C1' and (byres(Adjacent)))''','''"%s-%s"%(resn,resi)''') except: import tkMessageBox tkMessageBox.showinfo('Alert', "Select a motif first") #bind to menu for motifs def oxidoreductase(self, tag): if tag=='Superoxide Dismutase': self.superoxide() self.mot='superoxide' elif tag=='Peroxidase': self.peroxidase() self.mot='Peroxidase' elif tag=='Alcohol Dehydrogenase': self.alcoholdehyd() self.mot= 'alcoholdehyd' elif tag=='Aldose Reductase': self.aldoreductase() self.mot='aldoreductase' elif tag=='NAD Reductase': self.nadhbinder() self.mot='NAD-reductase' elif tag=='NAD Reductase2': self.nadhbinder2() self.mot='NAD-reductase2' elif tag=='Betaine aldehyde dehydrogenase': self.betainedehydrogenase() self.mot='betaine_dehydrogenase' def transferase(self, tag): if tag =='Amino Transferase': self.aminotransferase() self.mot='Aminotransferase' elif tag=='Glutamine Amidotransferase': self.glutamine_amidotransferase() self.mot='glu_amidotransferase' elif tag =='Thymidine Kinase': self.thymidinekinase() self.mot='Tkinase' elif tag =='ACTase': self.ACTase() self.mot='actase' elif tag=='Adenylate Kinase': self.adenylatekinase() self.mot='adenylatekinase' elif tag=='SRC Family Kinase': self.tyrosinekinase() self.mot='SRC-Kinase' elif tag=='Hhal Methyltransferase': self.hhal() self.mot='hhal' elif tag=='Serotonin Acetyltransferase': self.serotoninacetyl() self.mot = 'Serotonin_transferase' elif tag=='Cyclin Dependent Kinase': self.cyclinkinase() self.mot = 'Cyclin_Kinase' def hydrolase(self, tag): if tag =='Serine Protease': self.serineprotease() self.mot='serineprotease' elif tag == 'Papain Like': self.paplike() self.mot='paplike' elif tag == 'Metalloprotease': self.metalloprotease() self.mot='metalloprotease' elif tag == 'Tyrosine Phosphatase': self.tyrophos() self.mot= 'tyrophos' elif tag == 'Beta Lactamase': self.Blactamase() self.mot='lactamase' elif tag == 'O-Glycosyl': self.oglycosyl() self.mot='o-glycosyl' elif tag == 'Cephalosporin deacetylase': self.cephdeacetylase() self.mot='deacetylase' def lyase(self, tag): if tag =='Carbonic Anhydrase': self.carbanhyd() self.mot='carbonicanhydrase' elif tag=='Carbon Carbon': self.carboncarbon() self.mot='carboncarbon' elif tag=='Chondroitinase': self.chondrolyase() self.mot='chondroitinase' elif tag =='Hyaluronate-Lyase': self.hyaluronlyase() self.mot='Hyaluronate_Lyase' elif tag=='Exonuclease 3': self.exonucleaseiii() self.mot='Exonuclease3' elif tag=='Citrate Synthase': self.citratesynth() self.mot='Citrate_Synth' def isomerase(self, tag): if tag =='Fucose Isomerase': self.fisomerase() self.mot='fucoseisomerase' elif tag =='Triose Phosphate Isomerase': self.trioseisomerase() self.mot='TrioseIsomerase' elif tag=='FK506 Cis-Trans': self.cistransisomerase() self.mot='Cis-trans' def ligase(self, tag): if tag =='DNA Ligase': self.dnaligase() self.mot='ligase' def other(self, tag): if tag =='Zinc Finger': self.zincfinger() self.mot='Zinc_finger' #after appending motif to motif search field allows user to click on it #and run the motif function def allmotif(self): motif = self.motifbox.getcurselection() for item in motif: tag = item try: if len(tag) == 0: print 'No selection for double click' elif tag == '2-Cyclin Dependent Kinase': self.cyclinkinase() self.mot='Cyclin_Kinase' elif tag == '1-Cyclin Dependent Kinase': self.cyclinkinase() self.mot='Cyclin_Kinase' elif tag=='1-Betaine aldehyde dehydrogenase': self.betainedehydrogenase() self.mot='betaine_dehydrogenase' elif tag=='1-Betaine aldehyde dehydrogenase': self.betainedehydrogenase() self.mot='betaine_dehydrogenase' elif tag == '1-Serotonin Acetyltransferase': self.serotoninacetyl() self.mot='Serotonin_transferase' elif tag == '2-Serotonin Acetyltransferase': self.serotoninacetyl() self.mot='Serotonin_transferase' elif tag =='1-Zinc Finger': self.zincfinger() self.mot='Zinc_finger' elif tag =='1-DNA Ligase': self.dnaligase() self.mot='ligase' elif tag =='1-Fucose Isomerase': self.fisomerase() self.mot='fucoseisomerase' elif tag =='1-Triose Phosphate Isomerase': self.trioseisomerase() self.mot='TrioseIsomerase' elif tag=='1-FK506 Cis-Trans': self.cistransisomerase() self.mot='Cis-trans' elif tag =='1-Carbonic Anhydrase': self.carbanhyd() self.mot='carbonicanhydrase' elif tag=='1-Carbon Carbon': self.carboncarbon() self.mot='carboncarbon' elif tag=='1-Chondroitinase': self.chondrolyase() self.mot='chondroitinase' elif tag =='1-Hyaluronate-Lyase': self.hyaluronlyase() self.mot='Hyaluronate_Lyase' elif tag=='1-Exonuclease 3': self.exonucleaseiii() self.mot='Exonuclease3' elif tag=='1-Citrate Synthase': self.citratesynth() self.mot='Citrate_Synth' elif tag =='1-Serine Protease': self.serineprotease() self.mot='serineprotease' elif tag == '1-Papain Like': self.paplike() self.mot='paplike' elif tag == '1-Metalloprotease': self.metalloprotease() self.mot='metalloprotease' elif tag == '1-Tyrosine Phosphatase': self.tyrophos() self.mot= 'tyrophos' elif tag == '1-Beta Lactamase': self.Blactamase() self.mot='lactamase' elif tag == '1-O-Glycosyl': self.oglycosyl() self.mot='o-glycosyl' elif tag == '1-Cephalosporin deacetylase': self.cephdeacetylase() self.mot='deacetylase' elif tag =='1-Amino Transferase': self.aminotransferase() self.mot='Aminotransferase' elif tag=='1-Glutamine Amidotransferase': self.glutamine_amidotransferase() self.mot='glu_amidotransferase' elif tag =='1-Thymidine Kinase': self.thymidinekinase() self.mot='Tkinase' elif tag =='1-ACTase': self.ACTase() self.mot='actase' elif tag=='1-Adenylate Kinase': self.adenylatekinase() self.mot='adenylatekinase' elif tag=='1-SRC Family Kinase': self.tyrosinekinase() self.mot='SRC-Kinase' elif tag=='1-Hhal Methyltransferase': self.hhal() self.mot='hhal' elif tag=='1-Superoxide Dismutase': self.superoxide() self.mot='superoxide' elif tag=='1-Peroxidase': self.peroxidase() self.mot='Peroxidase' elif tag=='1-Alcohol Dehydrogenase': self.alcoholdehyd() self.mot= 'alcoholdehyd' elif tag=='1-Aldose Reductase': self.aldoreductase() self.mot='aldoreductase' elif tag=='1-NAD Reductase': self.nadhbinder() self.mot='NAD-reductase' elif tag=='1-NAD Reductase2': self.nadhbinder2() self.mot='NAD-reductase2' elif tag =='2-Zinc Finger': self.zincfinger() self.mot='Zinc_finger' elif tag =='2-DNA Ligase': self.dnaligase() self.mot='ligase' elif tag =='2-Fucose Isomerase': self.fisomerase() self.mot='fucoseisomerase' elif tag =='2-Triose Phosphate Isomerase': self.trioseisomerase() self.mot='TrioseIsomerase' elif tag=='2-FK506 Cis-Trans': self.cistransisomerase() self.mot='Cis-trans' elif tag =='2-Carbonic Anhydrase': self.carbanhyd() self.mot='carbonicanhydrase' elif tag=='2-Carbon Carbon': self.carboncarbon() self.mot='carboncarbon' elif tag=='2-Chondroitinase': self.chondrolyase() self.mot='chondroitinase' elif tag =='2-Hyaluronate-Lyase': self.hyaluronlyase() self.mot='Hyaluronate_Lyase' elif tag=='2-Exonuclease 3': self.exonucleaseiii() self.mot='Exonuclease3' elif tag=='2-Citrate Synthase': self.citratesynth() self.mot='Citrate_Synth' elif tag =='2-Serine Protease': self.serineprotease() self.mot='serineprotease' elif tag == '2-Papain Like': self.paplike() self.mot='paplike' elif tag == '2-Metalloprotease': self.metalloprotease() self.mot='metalloprotease' elif tag == '2-Tyrosine Phosphatase': self.tyrophos() self.mot= 'tyrophos' elif tag == '2-Beta Lactamase': self.Blactamase() self.mot='lactamase' elif tag == '2-O-Glycosyl': self.oglycosyl() self.mot='o-glycosyl' elif tag == '2-Cephalosporin deacetylase': self.cephdeacetylase() self.mot='deacetylase' elif tag =='2-Amino Transferase': self.aminotransferase() self.mot='Aminotransferase' elif tag=='2-Glutamine Amidotransferase': self.glutamine_amidotransferase() self.mot='glu_amidotransferase' elif tag =='2-Thymidine Kinase': self.thymidinekinase() self.mot='Tkinase' elif tag =='2-ACTase': self.ACTase() self.mot='actase' elif tag=='2-Adenylate Kinase': self.adenylatekinase() self.mot='adenylatekinase' elif tag=='2-SRC Family Kinase': self.tyrosinekinase() self.mot='SRC-Kinase' elif tag=='2-Hhal Methyltransferase': self.hhal() self.mot='hhal' elif tag=='2-Superoxide Dismutase': self.superoxide() self.mot='superoxide' elif tag=='2-Peroxidase': self.peroxidase() self.mot='Peroxidase' elif tag=='2-Alcohol Dehydrogenase': self.alcoholdehyd() self.mot= 'alcoholdehyd' elif tag=='2-Aldose Reductase': self.aldoreductase() self.mot='aldoreductase' elif tag=='2-NAD Reductase': self.nadhbinder() self.mot='NAD-reductase' elif tag=='2-NAD Reductase2': self.nadhbinder2() self.mot='NAD-reductase2' except: import tkMessageBox tkMessageBox.showinfo('Alert', 'There is no motif there') #def custom motif dropdown selection def set_motifA(self, tag): cmd.deselect() if tag=='gly': self.mA = 'gly' elif tag=='ala': self.mA = 'ala' elif tag=='val': self.mA = 'val' elif tag=='leu': self.mA = 'leu' elif tag=='ile': self.mA = 'ile' elif tag=='met': self.mA = 'met' elif tag=='pro': self.mA = 'pro' elif tag=='phe': self.mA = 'phe' elif tag=='tyr': self.mA = 'tyr' elif tag=='trp': self.mA = 'trp' elif tag=='ser': self.mA = 'ser' elif tag=='thr': self.mA = 'thr' elif tag=='cys': self.mA = 'cys' elif tag=='lys': self.mA = 'lys' elif tag=='arg': self.mA = 'arg' elif tag=='his': self.mA = 'his' elif tag=='asp': self.mA = 'asp' elif tag=='glu': self.mA = 'glu' elif tag=='asn': self.mA = 'asn' elif tag=='gln': self.mA = 'gln' def set_motifB(self, tag): cmd.deselect() if tag=='gly': self.mB = 'gly' elif tag=='ala': self.mB = 'ala' elif tag=='val': self.mB = 'val' elif tag=='leu': self.mB = 'leu' elif tag=='ile': self.mB = 'ile' elif tag=='met': self.mB = 'met' elif tag=='pro': self.mB = 'pro' elif tag=='phe': self.mB = 'phe' elif tag=='tyr': self.mB = 'tyr' elif tag=='trp': self.mB = 'trp' elif tag=='ser': self.mB = 'ser' elif tag=='thr': self.mB = 'thr' elif tag=='cys': self.mB = 'cys' elif tag=='lys': self.mB = 'lys' elif tag=='arg': self.mB = 'arg' elif tag=='his': self.mB = 'his' elif tag=='asp': self.mB = 'asp' elif tag=='glu': self.mB = 'glu' elif tag=='asn': self.mB = 'asn' elif tag=='gln': self.mB = 'gln' def set_motifC(self, tag): cmd.deselect() if tag=='gly': self.mC = 'gly' elif tag=='ala': self.mC = 'ala' elif tag=='val': self.mC = 'val' elif tag=='leu': self.mC = 'leu' elif tag=='ile': self.mC = 'ile' elif tag=='met': self.mC = 'met' elif tag=='pro': self.mC = 'pro' elif tag=='phe': self.mC = 'phe' elif tag=='tyr': self.mC = 'tyr' elif tag=='trp': self.mC = 'trp' elif tag=='ser': self.mC = 'ser' elif tag=='thr': self.mC = 'thr' elif tag=='cys': self.mC = 'cys' elif tag=='lys': self.mC = 'lys' elif tag=='arg': self.mC = 'arg' elif tag=='his': self.mC = 'his' elif tag=='asp': self.mC = 'asp' elif tag=='glu': self.mC = 'glu' elif tag=='asn': self.mC = 'asn' elif tag=='gln': self.mC = 'gln' def set_motifD(self, tag): cmd.deselect() if tag=='gly': self.mD = 'gly' elif tag=='ala': self.mD = 'ala' elif tag=='val': self.mD = 'val' elif tag=='leu': self.mD = 'leu' elif tag=='ile': self.mD = 'ile' elif tag=='met': self.mD = 'met' elif tag=='pro': self.mD = 'pro' elif tag=='phe': self.mD = 'phe' elif tag=='tyr': self.mD = 'tyr' elif tag=='trp': self.mD = 'trp' elif tag=='ser': self.mD = 'ser' elif tag=='thr': self.mD = 'thr' elif tag=='cys': self.mD = 'cys' elif tag=='lys': self.mD = 'lys' elif tag=='arg': self.mD = 'arg' elif tag=='his': self.mD = 'his' elif tag=='asp': self.mD = 'asp' elif tag=='glu': self.mD = 'glu' elif tag=='asn': self.mD = 'asn' elif tag=='gln': self.mD = 'gln' #def custom motif dropdown selection def set_motifAA(self, tag): cmd.deselect() if tag=='gly': self.mAA = 'gly' elif tag=='ala': self.mAA = 'ala' elif tag=='val': self.mAA = 'val' elif tag=='leu': self.mAA = 'leu' elif tag=='ile': self.mAA = 'ile' elif tag=='met': self.mAA = 'met' elif tag=='pro': self.mAA = 'pro' elif tag=='phe': self.mAA = 'phe' elif tag=='tyr': self.mAA = 'tyr' elif tag=='trp': self.mAA = 'trp' elif tag=='ser': self.mAA = 'ser' elif tag=='thr': self.mAA = 'thr' elif tag=='cys': self.mAA = 'cys' elif tag=='lys': self.mAA = 'lys' elif tag=='arg': self.mAA = 'arg' elif tag=='his': self.mAA = 'his' elif tag=='asp': self.mAA = 'asp' elif tag=='glu': self.mAA = 'glu' elif tag=='asn': self.mAA = 'asn' elif tag=='gln': self.mAA = 'gln' def set_motifAB(self, tag): cmd.deselect() if tag=='gly': self.mAB = 'gly' elif tag=='ala': self.mAB = 'ala' elif tag=='val': self.mAB = 'val' elif tag=='leu': self.mAB = 'leu' elif tag=='ile': self.mAB = 'ile' elif tag=='met': self.mAB = 'met' elif tag=='pro': self.mAB = 'pro' elif tag=='phe': self.mAB = 'phe' elif tag=='tyr': self.mAB = 'tyr' elif tag=='trp': self.mAB = 'trp' elif tag=='ser': self.mAB = 'ser' elif tag=='thr': self.mAB = 'thr' elif tag=='cys': self.mAB = 'cys' elif tag=='lys': self.mAB = 'lys' elif tag=='arg': self.mAB = 'arg' elif tag=='his': self.mAB = 'his' elif tag=='asp': self.mAB = 'asp' elif tag=='glu': self.mAB = 'glu' elif tag=='asn': self.mAB = 'asn' elif tag=='gln': self.mAB = 'gln' def set_motifAC(self, tag): cmd.deselect() if tag=='gly': self.mAC = 'gly' elif tag=='ala': self.mAC = 'ala' elif tag=='val': self.mAC = 'val' elif tag=='leu': self.mAC = 'leu' elif tag=='ile': self.mAC = 'ile' elif tag=='met': self.mAC = 'met' elif tag=='pro': self.mAC = 'pro' elif tag=='phe': self.mAC = 'phe' elif tag=='tyr': self.mAC = 'tyr' elif tag=='trp': self.mAC = 'trp' elif tag=='ser': self.mAC = 'ser' elif tag=='thr': self.mAC = 'thr' elif tag=='cys': self.mAC = 'cys' elif tag=='lys': self.mAC = 'lys' elif tag=='arg': self.mAC = 'arg' elif tag=='his': self.mAC = 'his' elif tag=='asp': self.mAC = 'asp' elif tag=='glu': self.mAC = 'glu' elif tag=='asn': self.mAC = 'asn' elif tag=='gln': self.mAC = 'gln' def set_motifAD(self, tag): cmd.deselect() if tag=='gly': self.mAD = 'gly' elif tag=='ala': self.mAD = 'ala' elif tag=='val': self.mAD = 'val' elif tag=='leu': self.mAD = 'leu' elif tag=='ile': self.mAD = 'ile' elif tag=='met': self.mAD = 'met' elif tag=='pro': self.mAD = 'pro' elif tag=='phe': self.mAD = 'phe' elif tag=='tyr': self.mAD = 'tyr' elif tag=='trp': self.mAD = 'trp' elif tag=='ser': self.mAD = 'ser' elif tag=='thr': self.mAD = 'thr' elif tag=='cys': self.mAD = 'cys' elif tag=='lys': self.mAD = 'lys' elif tag=='arg': self.mAD = 'arg' elif tag=='his': self.mAD = 'his' elif tag=='asp': self.mAD = 'asp' elif tag=='glu': self.mAD = 'glu' elif tag=='asn': self.mAD = 'asn' elif tag=='gln': self.mAD = 'gln' #Custom motif functions def bimotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mA = self.mA mB = self.mB cmd.do('sel AA, resn %s within %s of resn %s' % (mA, self.selA.get(), mB)) cmd.do('sel BB, resn %s within %s of resn %s' % (mB, self.selA.get(), mA)) cmd.select('motif', 'byres AA | byres BB') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A and B') def trimotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mA = self.mA mB = self.mB mC = self.mC cmd.do('sel AA, resn %s within %s of resn %s' % (mA, self.selA.get(), mB)) cmd.do('sel BB, resn %s within %s of resn %s' % (mB, self.selA.get(), mA)) cmd.do('sel CC, resn %s within %s of resn %s' % (mC, self.selB.get(), mB)) cmd.select('motif', 'byres AA | byres BB | byres CC') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') cmd.delete('CC') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A, B, and C') def quadmotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mA = self.mA mB = self.mB mC = self.mC mD = self.mD cmd.do('sel AA, resn %s within %s of resn %s' % (mA, self.selA.get(), mB)) cmd.do('sel BB, resn %s within %s of resn %s' % (mB, self.selA.get(), mA)) cmd.do('sel CC, resn %s within %s of resn %s' % (mC, self.selB.get(), mB)) cmd.do('sel DD, resn %s within %s of resn %s' % (mD, self.selC.get(), mC)) cmd.select('motif', 'byres AA | byres BB | byres CC') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') cmd.delete('CC') cmd.delete('DD') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A, B, C, and D') def Abimotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mAA = self.mAA mAB = self.mAB cmd.do('sel AA, resn %s within %s of resn %s' % (mAA, self.selAB.get(), mAB)) cmd.do('sel BB, resn %s within %s of resn %s' % (mAB, self.selAB.get(), mAA)) cmd.select('motif', 'byres AA | byres BB') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A and B') def Atrimotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mAA = self.mAA mAB = self.mAB mAC = self.mAC cmd.do('sel AA1, resn %s within %s of resn %s' % (mAA, self.selAB.get(), mAB)) cmd.select('AA2', 'resn %s within %s of resn %s' % (mAA, self.selAC.get(), mAC)) cmd.select('AA', 'byres AA1 and byres AA2') cmd.do('sel BB1, resn %s within %s of resn %s' % (mAB, self.selAB.get(), mAA)) cmd.select('BB2', 'resn %s within %s of resn %s' % (mAB, self.selBC.get(), mAC)) cmd.select('BB', 'byres BB1 and byres BB2') cmd.do('sel CC1, resn %s within %s of resn %s' % (mAC, self.selBC.get(), mAB)) cmd.select('CC2', 'resn %s within %s of resn %s' % (mAC, self.selAC.get(), mAA)) cmd.select('CC', 'byres CC1 and byres CC2') cmd.select('motif', 'byres AA | byres BB | byres CC') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') cmd.delete('CC') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A, B, and C') def Aquadmotif(self): try: self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() self.set_defaults() self.delcrea() cmd.delete('motif') cmd.hide('everything') mAA = self.mAA mAB = self.mAB mAC = self.mAC mAD = self.mAD cmd.do('sel AA1, resn %s within %s of resn %s' % (mAA, self.selAB.get(), mAB)) cmd.select('AA2', 'resn %s within %s of resn %s' % (mAA, self.selAC.get(), mAC)) cmd.select('AA3', 'resn %s within %s of resn %s' % (mAA, self.selAD.get(), mAD)) cmd.select('AA', 'byres AA1 and byres AA2 and byres AA3') cmd.do('sel BB1, resn %s within %s of resn %s' % (mAB, self.selAB.get(), mAA)) cmd.select('BB2', 'resn %s within %s of resn %s' % (mAB, self.selBC.get(), mAC)) cmd.select('BB3', 'resn %s within %s of resn %s' % (mAB, self.selBD.get(), mAD)) cmd.select('BB', 'byres BB1 and byres BB2 and byres BB3') cmd.do('sel CC1, resn %s within %s of resn %s' % (mAC, self.selBC.get(), mAB)) cmd.select('CC2', 'resn %s within %s of resn %s' % (mAC, self.selAC.get(), mAA)) cmd.select('CC3', 'resn %s within %s of resn %s' % (mAC, self.selCD.get(), mAD)) cmd.select('CC', 'byres CC1 and byres CC2 and byres CC3') cmd.do('sel DD1, resn %s within %s of resn %s' % (mAD, self.selAD.get(), mAA)) cmd.select('DD2', 'resn %s within %s of resn %s' % (mAD, self.selBD.get(), mAB)) cmd.select('DD3', 'resn %s within %s of resn %s' % (mAD, self.selCD.get(), mAC)) cmd.select('DD', 'byres DD1 and byres DD2 and byres DD3') cmd.select('motif', 'byres AA | byres BB | byres CC | byres DD') cmd.show('cartoon', 'all') cmd.set('cartoon_transparency', '0.5', 'all') cmd.show('sticks', 'motif') cmd.set('stick_radius','0.5') self.cpkmotif() cmd.orient('motif') cmd.deselect() cmd.delete('AA') cmd.delete('BB') cmd.delete('CC') cmd.delete('DD') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must select an amino acid for menus A, B, C, and D') #reset the range sliders def resetmotif(self): self.selA.set(4.0) self.selB.set(4.0) self.selC.set(4.0) self.selAB.set(4.0) self.selAC.set(4.0) self.selAD.set(4.0) self.selBC.set(4.0) self.selBD.set(4.0) self.selCD.set(4.0) def resetrange(self): self.range.set(1.0) def setcusmotif(self): a = [] for object in os.listdir('./modules/pmg_tk/startup/Motifs'): a.append(object) self.motifdrop.setlist(a) def runcusmotif(self): a = [''] for object in os.listdir('./modules/pmg_tk/startup/Motifs'): a.append(object) motif = self.motifdrop.getcurselection() for item in motif: tag = item try: for i in range(1, 100, 1): if a[i] in tag: cmd.do('run ./modules/pmg_tk/startup/Motifs/'+a[i]) except: pass #No more motifs......Hurray #--------------------------------------# # # #COMMANDS" TAB METHODS # # # #--------------------------------------# # Color the molecule def color_cpk(self, str ): cmd.color("carbgray", "(elem C)" + str ) cmd.color("red", "elem O" + str ) cmd.color("white", "elem H" + str ) cmd.color("nitblue", "elem N" + str ) cmd.color("sulfyellow", "elem S" + str ) cmd.color("phosorange", "elem P+Fe+Ba" + str ) cmd.color("green", "elem Cl+B" + str ) cmd.color("brown", "elem Br+Zn+Cu+Ni" + str ) cmd.color("blue", "elem Na" + str ) cmd.color("forest", "elem Mg" + str ) cmd.color("darkgray", "elem Ca+Mn+Al+Ti+Cr+Ag" + str ) cmd.color("goldenrod", "elem Au+F+Si" + str) cmd.color("ipurple", "elem I" + str) cmd.color("firebrick", "elem Li" + str) cmd.color("helpink", "elem He" + str) if self.script=='1': self.f.write('''cmd.color("carbgray", "(elem C)" + str ) cmd.color("red", "elem O" + str ) cmd.color("white", "elem H" + str ) cmd.color("nitblue", "elem N" + str ) cmd.color("sulfyellow", "elem S" + str ) cmd.color("phosorange", "elem P+Fe+Ba" + str ) cmd.color("green", "elem Cl+B" + str ) cmd.color("brown", "elem Br+Zn+Cu+Ni" + str ) cmd.color("blue", "elem Na" + str ) cmd.color("forest", "elem Mg" + str ) cmd.color("darkgray", "elem Ca+Mn+Al+Ti+Cr+Ag" + str ) cmd.color("goldenrod", "elem Au+F+Si" + str) cmd.color("ipurple", "elem I" + str) cmd.color("firebrick", "elem Li" + str) cmd.color("helpink", "elem He" + str)\n''') # Attempt to simulate the default PyMOL colorings def color_default(self): cmd.color("green", "elem C") cmd.color("red", "elem O") cmd.color("blue", "elem N") if self.script=='1': self.f.write('''cmd.color("green", "elem C") cmd.color("red", "elem O") cmd.color("blue", "elem N")\n''') # Show ligands as spheres def space_fill_ligand(self): cmd.select("Bad", "resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR+ACD+ACE+ALB+ALI+ABU+ARO+ASX+BAS+BET+FOR+GLX+HET+HSE+HYP+HYL+ORN+PCA+SAR+TAU+TER+THY+UNK+a+g+c+t+u+HOH+MSE") cmd.select("ligand","!Bad") cmd.hide("everything", "ligand") cmd.show("spheres", "ligand") cmd.delete("Bad") if self.script=='1': self.f.write('''cmd.select("Bad", "resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR+ACD+ACE+ALB+ALI+ABU+ARO+ASX+BAS+BET+FOR+GLX+HET+HSE+HYP+HYL+ORN+PCA+SAR+TAU+TER+THY+UNK+a+g+c+t+u+HOH+MSE") cmd.select("ligand","!Bad") cmd.hide("everything", "ligand") cmd.show("spheres", "ligand") cmd.delete("Bad")\n''') self.cpkligands() cmd.deselect() # create additional colors # (adopted from some code written by # Kevin Galens and Jamie Duke at RIT) def init_color(self): cmd.set_color("sulfyellow", "[ 1.00, 0.78, 0.20 ]") cmd.set_color("carbgray", "[ 0.78, 0.78, 0.78 ]") cmd.set_color("nitblue", "[ 0.56, 0.56, 1.00 ]") cmd.set_color("phosorange", "[ 1.00, 0.65, 0.00 ]") cmd.set_color("znbrown", "[ 0.65, 0.16, 0.16 ]") cmd.set_color("goldenrod", "[ 0.85, 0.65, 0.125 ]") cmd.set_color("ipurple", "[ 0.63, 0.125, 0.94 ]") cmd.set_color("helpink", "[ 1.00, 0.75, 0.80 ]") cmd.set_color("darkgray", "[ 0.5, 0.5, 0.56 ]") # Show/Hide ALL representations def show_all(self, tag): list = self.rep1.getvalue() list2 = self.rep2.getvalue() if tag == 'Show all': self.rep1.invoke('Lines') self.rep1.invoke('Sticks') self.rep1.invoke('Ribbons') self.rep1.invoke('Cartoon') self.rep2.invoke('Dots') self.rep2.invoke('Spheres') self.rep2.invoke('Mesh') self.rep2.invoke('Surface') for item in list: self.rep1.invoke(item) for item in list2: self.rep2.invoke(item) cmd.do('show everything') if self.script=='1': self.f.write('''cmd.do('show everything')\n''') else: cmd.do('hide everything') if self.script=='1': self.f.write('''cmd.do('show everything')\n''') for item in list: self.rep1.invoke(item) for item in list2: self.rep2.invoke(item) # Show individual representations def show_rep(self, tag): try: sel = self.sel if tag == 'Lines': cmd.show('lines',sel) if self.script=='1': self.f.write('cmd.show('"lines"',"'+sel+'")\n') elif tag == 'Sticks': cmd.show('sticks', sel) if self.script=='1': self.f.write('cmd.show('"sticks"',"'+sel+'")\n') elif tag == 'Ribbons': cmd.show('ribbon', sel) if self.script=='1': self.f.write('cmd.show('"ribbon"',"'+sel+'")\n') elif tag == 'Cartoon': cmd.show('cartoon', sel) if self.script=='1': self.f.write('cmd.show('"cartoon"',"'+sel+'")\n') elif tag == 'Dots': cmd.show('dots', sel) if self.script=='1': self.f.write('cmd.show('"dots"',"'+sel+'")\n') elif tag == 'Spheres': cmd.show('spheres', sel) if self.script=='1': self.f.write('cmd.show('"spheres"',"'+sel+'")\n') elif tag == 'Mesh': cmd.show('mesh', sel) if self.script=='1': self.f.write('cmd.show('"mesh"',"'+sel+'")\n') elif tag == 'Surface': cmd.show('surface', sel) if self.script=='1': self.f.write('cmd.show('"surface"',"'+sel+'")\n') elif tag == 'Water': cmd.show('(resn HOH)') cmd.show('spheres', '(resn HOH)') if self.script=='1': self.f.write('''cmd.show('(resn HOH)') cmd.show('spheres', '(resn HOH)')\n''') elif tag=='Ball and Stick': cmd.set('sphere_scale', '0.35', sel) cmd.show('spheres',sel) cmd.show('sticks',sel) if self.script=='1': self.f.write('''cmd.set('sphere_scale', '0.35', "'''+sel+'''") cmd.show('spheres',"'''+sel+'''") cmd.show('sticks',"'''+sel+'''")\n''') elif tag=='Polar Contacts': cmd.dist(sel+"_polar_conts",sel,sel,quiet=1,mode=2,label=0,reset=1) cmd.enable(sel+"1CHO_polar_conts") if self.script=='1': self.f.write('''cmd.dist(sel+"_polar_conts","'''+sel+'''","'''+sel+'''",quiet=1,mode=2,label=0,reset=1) cmd.enable('''+sel+'''"1CHO_polar_conts")\n''') except: import tkMessageBox tkMessageBox.showinfo('Error', 'Update Selection!') # Hide individual representations def hide_rep(self, tag): try: sel = self.sel if tag == 'Lines': cmd.hide('lines',sel) if self.script=='1': self.f.write('''cmd.hide('lines',"'''+sel+'''")\n''') elif tag == 'Sticks': cmd.hide('sticks', sel) if self.script=='1': self.f.write('''cmd.hide('sticks',"'''+sel+'''")\n''') elif tag == 'Ribbons': cmd.hide('ribbon', sel) if self.script=='1': self.f.write('''cmd.hide('ribbon',"'''+sel+'''")\n''') elif tag == 'Cartoon': cmd.hide('cartoon', sel) if self.script=='1': self.f.write('''cmd.hide('cartoon',"'''+sel+'''")\n''') elif tag == 'Dots': cmd.hide('dots', sel) if self.script=='1': self.f.write('''cmd.hide('dots',"'''+sel+'''")\n''') elif tag == 'Spheres': cmd.hide('spheres', sel) if self.script=='1': self.f.write('''cmd.hide('spheres',"'''+sel+'''")\n''') elif tag == 'Mesh': cmd.hide('mesh', sel) if self.script=='1': self.f.write('''cmd.hide('mesh',"'''+sel+'''")\n''') elif tag == 'Surface': cmd.hide('surface', sel) if self.script=='1': self.f.write('''cmd.hide('surface',"'''+sel+'''")\n''') elif tag == 'Water': cmd.hide('(resn HOH)') if self.script=='1': self.f.write('''cmd.hide('(resn HOH)')\n''') elif tag == 'Everything': cmd.hide('everything', sel) if self.script=='1': self.f.write('''cmd.hide('everything',"'''+sel+'''")\n''') elif tag=='Ball and Stick': cmd.hide('spheres',sel) cmd.hide('sticks',sel) if self.script=='1': self.f.write('''cmd.hide('spheres',"'''+sel+'''")\n''') if self.script=='1': self.f.write('''cmd.hide('sticks',"'''+sel+'''")\n''') elif tag =='Polar Contacts': cmd.delete(sel+"_polar_conts") if self.script=='1': self.f.write(''' cmd.delete("'''+sel+'''_polar_conts")\n''') except: import tkMessageBox tkMessageBox.showinfo('Error', 'Update Selection!') #-------------Version 2--------------# # Set selection of atoms # - initial selection is 'all' def set_sel(self, tag): cmd.deselect() c=re.compile("^Chain") if tag=='All': self.sel = 'all' elif tag=='protein': self.sel = 'protein' elif tag=='nucleic_acid': self.sel = 'nucleic_acid' elif tag=='ligands': self.sel = 'ligands' elif tag=='heme': self.sel = 'heme' elif tag=='Chain-A': self.sel=('Chain-A') elif tag=='Chain-A': self.sel=('Chain-A') elif tag=='Chain-B': self.sel=('Chain-B') elif tag=='Chain-C': self.sel=('Chain-C') elif tag=='Chain-D': self.sel=('Chain-D') elif tag=='Chain-E': self.sel=('Chain-E') elif tag=='Chain-F': self.sel=('Chain-F') elif tag=='Chain-G': self.sel=('Chain-G') elif tag=='Chain-H': self.sel=('Chain-H') elif tag=='Chain-I': self.sel=('Chain-I') elif tag=='Chain-J': self.sel=('Chain-J') elif tag=='Chain-K': self.sel=('Chain-K') elif tag=='Chain-L': self.sel=('Chain-L') elif tag=='Chain-M': self.sel=('Chain-M') elif tag=='Chain-N': self.sel=('Chain-N') elif tag=='Chain-O': self.sel=('Chain-O') elif tag=='Chain-P': self.sel=('Chain-P') elif tag=='Chain-Q': self.sel=('Chain-Q') elif tag=='Chain-R': self.sel=('Chain-R') elif tag=='Chain-S': self.sel=('Chain-S') elif tag=='Chain-T': self.sel=('Chain-T') elif tag=='Chain-U': self.sel=('Chain-U') elif tag=='Chain-V': self.sel=('Chain-V') elif tag=='Chain-W': self.sel=('Chain-W') elif tag=='Chain-X': self.sel=('Chain-X') elif tag=='Chain-Y': self.sel=('Chain-Y') elif tag=='Chain-Z': self.sel=('Chain-Z') elif tag=='Not Selected': try: cmd.select('selection', '!sele') cmd.deselect() self.sel= 'selection' except: import tkMessageBox tkMessageBox.showinfo("Error", 'No selection has been made') elif tag=='hydrophobic': self.sel='hydrophobic' elif tag=='hydrophilic': self.sel='hydrophilic' elif tag=='acidic': self.sel='acidic' elif tag=='basic': self.sel='basic' # Set selection of atoms # - initial selection is 'all' def set_sel1(self, tag): cmd.deselect() c=re.compile("^Chain") if tag=='All': self.sel1 = 'all' elif tag=='protein': self.sel1 = 'protein' elif tag=='nucleic_acid': self.sel1 = 'nucleic_acid' elif tag=='ligands': self.sel1 = 'ligands' elif tag=='heme': self.sel1 = 'heme' elif tag=='Chain-A': self.sel1=('Chain-A') elif tag=='Chain-A': self.sel1=('Chain-A') elif tag=='Chain-B': self.sel1=('Chain-B') elif tag=='Chain-C': self.sel1=('Chain-C') elif tag=='Chain-D': self.sel1=('Chain-D') elif tag=='Chain-E': self.sel1=('Chain-E') elif tag=='Chain-F': self.sel1=('Chain-F') elif tag=='Chain-G': self.sel1=('Chain-G') elif tag=='Chain-H': self.sel1=('Chain-H') elif tag=='Chain-I': self.sel1=('Chain-I') elif tag=='Chain-J': self.sel1=('Chain-J') elif tag=='Chain-K': self.sel1=('Chain-K') elif tag=='Chain-L': self.sel1=('Chain-L') elif tag=='Chain-M': self.sel1=('Chain-M') elif tag=='Chain-N': self.sel1=('Chain-N') elif tag=='Chain-O': self.sel1=('Chain-O') elif tag=='Chain-P': self.sel1=('Chain-P') elif tag=='Chain-Q': self.sel1=('Chain-Q') elif tag=='Chain-R': self.sel1=('Chain-R') elif tag=='Chain-S': self.sel1=('Chain-S') elif tag=='Chain-T': self.sel1=('Chain-T') elif tag=='Chain-U': self.sel1=('Chain-U') elif tag=='Chain-V': self.sel1=('Chain-V') elif tag=='Chain-W': self.sel1=('Chain-W') elif tag=='Chain-X': self.sel1=('Chain-X') elif tag=='Chain-Y': self.sel1=('Chain-Y') elif tag=='Chain-Z': self.sel1=('Chain-Z') elif tag=='Not Selected': cmd.select('selection', '!sele') cmd.deselect() self.sel1= 'selection' elif tag=='hydrophobic': self.sel1='hydrophobic' elif tag=='hydrophilic': self.sel1='hydrophilic' elif tag=='acidic': self.sel1='acidic' elif tag=='basic': self.sel1='basic' #preset menubar link functions def presurf(self, tag): if tag=='Surface': self.surface_view() elif tag=='Surface on Cartoon': self.surf_toon() elif tag=='Surface on Sticks': self.surf_stick() elif tag=='Surface on Spheres': self.spheresurf() elif tag=='Mesh on Sticks': self.mesh_stick() elif tag=='Dots on Lines': self.dot_line() def pretoon(self, tag): if tag=='Cartoon': self.std_view() elif tag=='Putty': self.show_putty() elif tag=='Lines on Cartoon': self.stick_toon() elif tag=='Color by Chain': self.color_by_chain() def preres(self, tag): if tag=='Aromatics': self.color_aromatics() elif tag=='Show Charged': self.show_charged() elif tag=='Solubility': self.view_polarity() def prerov(self, tag): if tag=='Roving Sticks': self.rovingstickers() elif tag=='Roving Ball&Sticks': self.rovingballstick() elif tag=='Roving Spheres': self.rovingspheres() elif tag=='Roving Lines': self.rovinglines() def preele(self, tag): if tag=='Mesh on Ribbon': self.mesh_ribbon() elif tag=='Dots on Sticks': self.dot_sticks() elif tag=='Surface on Lines': self.surfinglines() def premisc(self, tag): if tag=='Hetero Atoms': self.show_hetero() elif tag=='Chain Contacts': self.chain_contact() elif tag=='DNA & RNA': self.show_dna_rna() elif tag=='CPK': self.show_cpk() elif tag=='Ball & Stick': self.ball_and_stick() def premovie(self, tag): if tag=='Ligand Zoom': self.ligandZoom() elif tag=='Build Protein': self.growProtein() elif tag=='Highlight Chains': self.highlight_chains() elif tag=='Rotate': self.rotate_y() elif tag=='Chain Pull': self.chain_pull() elif tag=='Ligand Pull': self.Ligand_Pull() elif tag=='Surface to Stick': self.surface_stick() elif tag=='Surface to Cartoon': self.surface_cartoon() elif tag=='Play': self.play() elif tag=='Stop': self.stop() elif tag=='Rewind': self.rewind() #------------------Version 1--------------# # Tell our command line what type of commands to read def set_cmd_type(self, tag): if tag == 'PyMOL': self.commandLine.setvalue('Enter PyMOL Commands Here') self.cmdType = 'PyMOL' else: self.commandLine.setvalue('Enter Chime Commands Here') self.cmdType = 'Chime' # Read commands from command line def command_line(self): try: command = self.commandLine.getvalue() if self.cmdType == 'PyMOL': cmd.do(command) self.commandLine.clear() else: self.converter.parseIt(command, self.commandLine, self.output) except: import tkMessageBox tkMessageBox.showinfo('Error', 'Invalid command or you must load the PDB through Pro-MOL') # Coloring on Selection def color_sel(self, tag): try: sel=self.sel if tag=='Red': cmd.color('red', sel) if self.script=='1': self.f.write('''cmd.color('red', '''+sel+'''")\n''') elif tag=='Green': cmd.color('green', sel) if self.script=='1': self.f.write('''cmd.color('green', '''+sel+'''")\n''') elif tag=='Orange': cmd.color('orange', sel) if self.script=='1': self.f.write('''cmd.color('orange', '''+sel+'''")\n''') elif tag=='Yellow': cmd.color('yellow', sel) if self.script=='1': self.f.write('''cmd.color('yellow', '''+sel+'''")\n''') elif tag=='Blue': cmd.color('blue', sel) if self.script=='1': self.f.write('''cmd.color('blue', '''+sel+'''")\n''') elif tag=='Violet': cmd.color('violet', sel) if self.script=='1': self.f.write('''cmd.color('violet', '''+sel+'''")\n''') elif tag=='CPK': cmd.color("oxygen","(elem O and "+sel+")") cmd.color("nitrogen","(elem N and "+sel+")") cmd.color("sulfur","(elem S and "+sel+")") cmd.color("hydrogen","(elem H and "+sel+")") cmd.color("gray","(elem C and "+sel+")") if self.script=='1': self.f.write('''cmd.color("oxygen","(elem O and "'''+sel+'''")") cmd.color("nitrogen","(elem N and "'''+sel+'''")") cmd.color("sulfur","(elem S and "'''+sel+'''")") cmd.color("hydrogen","(elem H and "'''+sel+'''")") cmd.color("gray","(elem C and "'''+sel+'''")")\n''') elif tag=='Other': color=tkColorChooser.askcolor(parent=self.int, title="Selection Color Chooser") colorArray =[] if color[0]!= None: list=color[0] print list for each in list: z = (each/255.0) val=repr(z) colorArray.append(val) cmd.set_color('newcolor', colorArray) cmd.color('newcolor', sel) except: import tkMessageBox tkMessageBox.showinfo('Error', 'Update Selection!') #------------------Version 2-----------------# #--------------------------------------# # # # SAVE METHODS # # # #--------------------------------------# def imgSave(self): import tkFileDialog file = tkFileDialog.asksaveasfilename(defaultextension=".png", initialdir="./PyMOL/") if len(file)>0: cmd.save(file) #------ #Brett and Charlie's (first attempt) code-------- #--Ray tracing with an auto calculator for height and width---- def imgraysave(self): import tkFileDialog root = Tk() root.geometry('226x147+140+140') root.title('Ray Trace') msg = Message(root, width = 200, text="You must Ray Trace before saving for a higher resolution image ") msg.place(x=5, y=5) a_label = Label(root, text = "Width") name1 = Entry(root, width = 12,) name1.insert(0, 640) b_label = Label(root, text = "Height") name2 = Entry(root, width = 12,) a_button = Button(root, text = "Ray Trace") a_label.place(x=10,y=50) b_button = Button(root, text = "Save") name1.place(x=50,y=50) b_label.place(x=10,y=80) name2.place(x=50,y=80) name2.insert(0, 480) a_button.place(x=10,y=110) b_button.place(x=80,y=110) c_button = Button(root, text = "Auto Calc") c_button.place(x=150,y=64) d_button = Button(root, text = 'Help') d_button.place(x = 150, y=110) d_button.configure(width = "8") b_button.configure(width = "8") a_button.configure(width = "8") c_button.configure(width = "8") #Help Message Box def rthelp(event): import tkFileDialog import tkMessageBox tkMessageBox.showinfo("Help","To save a higher resolution image you \nmust input width and height paramaters.\n \nOr input just width or just height and\n use the Auto Calc button to get the other.\n\n Paramaters should be under 5 digits\n or else Ray Trace may take a long time. \n \nThen click Save to save your image.") root.mainloop() d_button.bind('', rthelp) #Auto Calc Function def autocalc(event): try: if len(name1.get()) >= 1: name2.delete(0,20) name2.insert(0, int(int(name1.get())*.75)) elif len(name2.get()) >= 1: name1.delete(0,20) name1.insert(0, int(int(name2.get())*1.3333333333333333333333333333)) except: import tkFileDialog import tkMessageBox tkMessageBox.showinfo("Error", "Enter an integer value for width or height") root.mainloop() c_button.bind('',autocalc) #Defines ray trace function def raytrace(event): try: if len(name1.get()) > 3: import tkFileDialog import tkMessageBox tkMessageBox.showinfo("Ray Trace","You have entered a large value. Please be patient.\nClick OK to continue.") cmd.ray(name1.get(),name2.get()) root.mainloop() else: cmd.ray(name1.get(),name2.get()) root.mainloop() except: import tkFileDialog import tkMessageBox tkMessageBox.showinfo("Error", "Enter an integer value for width and height") root.mainloop() def savestop(event): file = tkFileDialog.asksaveasfilename(defaultextension=".png", initialdir="./PyMOL/") if len(file)>0: cmd.save(file) root.destroy() a_button.bind('',raytrace) b_button.bind('',savestop) root.mainloop() #---------Version 1---------------# #For future modifications---->Better to use Tcl/Tk methods instead of #Megawidgets for button creations and GUI manipulation, not enough time to #completely redo though #--------------------------------------# # # # UTILITY METHODS # # # #--------------------------------------# # ADD BUTTONS # Create and add buttons to the GUI def buttonAdd(self,frame,text,size,cmd,gridrow,gridcol,gridstick): #the button newBtn = Button(frame, text=text,highlightthickness=0, width=size,command=cmd,padx=0,pady=0) # add it to the gui newBtn.grid(row=gridrow, column=gridcol, sticky=gridstick, padx=2, pady=2) # ADD RADIO BUTTONS # Create and add radio buttons to the GUI def radioAdd(self,frame,pos,orient,cmd,label,btn_labels, gridrow, gridcol, cspan, rspan, gridstick): labels = btn_labels #the list of labels passed in by the user # create the radio button newRadio = Pmw.RadioSelect(frame, labelpos=pos, labelmargin=0, buttontype='radiobutton', orient=orient, label_text=label, command=cmd) # add it to the gui newRadio.grid(row=gridrow, column=gridcol, columnspan=cspan, rowspan=rspan, sticky=gridstick, padx=5) # add text to the buttons for text in labels: newRadio.add(text) newRadio.setvalue(labels[0]) # ADD FORMATTING SPACERS # Add white space to the GUI (used in formatting) def addSpace(self,frame,gridrow, gridcol): # create the button space = Label(frame, text=' ') space.grid(row=gridrow, column=gridcol) #--------------------------------------# # # # Display METHODS # # # #--------------------------------------# # handle stereo commands def stereo_switch(self, tag): if tag == 'Off': cmd.stereo('off') if self.script=='1': self.f.write('''cmd.stereo('off')\n''') elif tag == 'Quad': cmd.stereo('off') cmd.stereo('cross') cmd.stereo('quadbuffer') cmd.stereo('on') if self.script=='1': self.f.write('''cmd.stereo('off') cmd.stereo('cross') cmd.stereo('quadbuffer') cmd.stereo('on')\n''') elif tag == 'Cross-Eye': cmd.stereo('off') cmd.stereo('cross') cmd.stereo('on') if self.script=='1': self.f.write('''cmd.stereo('off') cmd.stereo('cross') cmd.stereo('on')\n''') else: cmd.stereo('off') cmd.stereo('walleye') cmd.stereo('on') if self.script=='1': self.f.write('''cmd.stereo('off') cmd.stereo('walleye') cmd.stereo('on')\n''') # change background colors def bgcolor_switch(self, tag): if tag == 'Black': cmd.do('bg_color black') if self.script=='1': self.f.write('''cmd.do('bg_color black')\n''') elif tag == 'White': cmd.do('bg_color white') if self.script=='1': self.f.write('''cmd.do('bg_color white')\n''') elif tag == 'Grey': cmd.do('bg_color grey') if self.script=='1': self.f.write('''cmd.do('bg_color grey')\n''') elif tag == 'Other': color=tkColorChooser.askcolor(parent=self.int, title="Background Color Chooser") colorArray =[] if color[0]!= None: list=color[0] print list for each in list: z = (each/255.0) val=repr(z) colorArray.append(val) cmd.set_color('newcolor', colorArray) cmd.do('bg_color newcolor') if self.script=='1': self.f.write('''cmd.set_color('newcolor', '''+colorArray+'''') cmd.do('bg_color newcolor')\n''') else: self.do_nothing() # change the color space def cspace_switch(self, tag): if tag == 'PyMOL': cmd.space('pymol') if self.script=='1': self.f.write('''cmd.space('pymol')\n''') elif tag == 'Publications': cmd.space('rgb') if self.script=='1': self.f.write('''cmd.space('rgb')\n''') else: cmd.space('cmyk') if self.script=='1': self.f.write('''cmd.space('cmyk')\n''') # hide/show interface def hide_interface(self, tag): if tag == 'Show': cmd.set('internal_gui','1') else: cmd.set('internal_gui','0') # Show/Hide Water def show_hide_water(self, tag): if tag == 'Show': cmd.show('(resn HOH)') cmd.show('spheres', '(resn HOH)') if self.script=='1': self.f.write('''cmd.show('(resn HOH)') cmd.show('spheres', '(resn HOH)')\n''') else: cmd.hide('(resn HOH)') if self.script=='1': self.f.write('''cmd.hide('(resn HOH)')\n''') #--------------------------------------# # # # PARSING METHODS # # # #--------------------------------------# # Sequence Getter def seqGetter(self, id): seq = self.p.chains[id] seq=string.upper(seq) seqArray=string.split(seq, ' ') if len(seqArray[0])==1: if seq[0]=='U': type ='RNA' if string.find(seq,'U')!=-1: type ='RNA' else: type = 'DNA' seq=string.replace(seq," ", "") else: type='Protein' info = "Chain "+id+"\nSequence Type: "+type+"\nSequence: "+seq self.info.config(state=NORMAL) self.info.delete(1.0,END) self.info.insert(END, info) self.info.config(state=DISABLED) return type #--------------------------------------# # # # MOVIE METHODS # # # #--------------------------------------# def rotate_y(self): cmd.mset() cmd.mset('1','180') cmd.util.mroll('1','180','1') cmd.mplay() # Movie to show locations of each of the chains in the molecule #does not run on external pdbs - Brett def highlight_chains(self): self.delcrea() cmd.mstop() cmd.mclear() cmd.mset() self.set_defaults() colors = ['blue','orange','silver','green','yellow', 'purple','brightorange','lightblue','lightorange', 'pink','forest','firebrick','paleyellow','salmon', 'ruby','wheat','lightmagenta','nitblue'] numChains = len(self.p.chains) numFrames = (numChains*200)+70 cmd.mset('1',numFrames) cmd.do('mdo 1: color red, all; hide cartoon, all') cmd.orient() cmd.mview('store','1') colorCount = 0 frameCount = 1 for i in self.p.chains.keys(): cmd.orient('chain ' + i) cmd.mview('store', frameCount+59) cmd.mview('store', frameCount+115) self.flash_chain(i, frameCount+59, 'red', colors[colorCount]) cmd.orient() cmd.turn('x','270') cmd.turn('y','180') cmd.mview('store',frameCount+150) cmd.mview('store',frameCount+170) colorCount += 1 frameCount += 200 if(frameCount > numFrames-100): cmd.orient() cmd.do('mdo '+str(numFrames)+': mstop') cmd.mview('store',(numChains*200)+70) cmd.mview('interpolate') cmd.show('ribbon') #cmd.show('surface') cmd.color('red','all') #cmd.set('transparency','0.75','all') #cmd.set('cartoon_transparency','0.0','all') # flash the chains on and off, eventually changing the color # (utilized by the highlight_chains method) def flash_chain(self, chainID, frame, initialColor, afterColor): cmd.do('mdo ' + str(frame)+': show cartoon, chain ' + str(chainID)) cmd.do('mdo '+str(frame+7)+': color '+afterColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+14)+': color '+initialColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+21)+': color '+afterColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+28)+': color '+initialColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+35)+': color '+afterColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+42)+': color '+initialColor+', chain '+str(chainID)) cmd.do('mdo '+str(frame+49)+': color '+afterColor+', chain '+str(chainID)) #does not run on external pdbs def ligandZoom(self): try: self.delcrea() import tkMessageBox cmd.mstop() cmd.mclear() cmd.mset() q=360 ids = self.p.idList if len(ids)==0: tkMessageBox.showinfo("Ligand Zoom", "Sorry this PDB file contains no ligands and cannot be made into a movie") else: objects = cmd.get_names('all') self.set_defaults() ids.sort() numFrames = 600+(335*(len(ids))) cmd.deselect() cmd.do('bg_color white') cmd.cartoon('tube', 'all') cmd.mset('1', numFrames) cmd.do('mdo 1: show cartoon, all; hide cartoon, resn a+t+c+g; show sticks, resn a+t+c+g;') cmd.reset() cmd.do('turn x, 180') cmd.orient() cmd.mview('store', '1') cmd.do('turn y, 180') cmd.mview('store', '120') cmd.mview('store', '150') cmd.do('turn y, 180') cmd.mview('store', '240') cmd.mview('store', '270') for i in range(len(ids)): self.color_cpk(' and (byres (ligands and '+ids[i]+')around 5)') self.color_cpk(' and ligands') cmd.orient('(ligands and '+ids[i]+')around 7') cmd.mview('store', str(q)) cmd.do('mdo '+str((q+1))+':set sphere_transparency, 0.1, ligands; set cartoon_transparency, 0.9, all; show spheres, (ligands and '+ids[i]+'); show sticks, (ligands and '+ids[i]+');') cmd.mview('store', str(q+10)) cmd.do('mdo '+str((q+11))+':set sphere_transparency, 0.2, ligands;') cmd.mview('store', str(q+20)) cmd.do('mdo '+str((q+21))+':set sphere_transparency, 0.3, ligands;') cmd.mview('store', str(q+30)) cmd.do('mdo '+str((q+31))+':set sphere_transparency, 0.4, ligands;') cmd.mview('store', str(q+40)) cmd.do('mdo '+str((q+41))+':set sphere_transparency, 0.5, ligands;') cmd.mview('store', str(q+50)) cmd.do('mdo '+str((q+51))+':show sticks, (byres (ligands and '+ids[i]+')around 1);') cmd.mview('store', str(q+60)) cmd.do('mdo '+str((q+61))+':show sticks, (byres (ligands and '+ids[i]+')around 2);') cmd.mview('store', str(q+70)) cmd.do('mdo '+str((q+71))+':show sticks, (byres (ligands and '+ids[i]+')around 3);') cmd.mview('store', str(q+80)) cmd.do('mdo '+str((q+81))+':show sticks, (byres (ligands and '+ids[i]+')around 4);') cmd.mview('store', str(q+81)) cmd.do('turn y, 180') cmd.mview('store', str(q+125)) cmd.mview('store', str(q+150)) cmd.do('mdo '+str((q+151))+': set cartoon_transparency, 0, all;') cmd.reset() cmd.orient() cmd.mview('store', str(q+215)) cmd.mview('store', str(q+255)) if i==(len(ids)-1): cmd.reset() cmd.orient() cmd.do('turn x, 180') cmd.mview('store', str(numFrames)) else: cmd.mview('store', str(q+335)) q=q+335 cmd.do('mdo '+str(numFrames)+': hide spheres, ligands; hide sticks, ligands around 4; label ligands, \' \'') cmd.do('mdo '+str(numFrames)+': mstop') cmd.mview('interpolate') cmd.rewind() except: import tkMessageBox tkMessageBox.showinfo('Error', 'You must open the PDB file through Pro-MOL') #fixed to work on externally loaded pdbs by Brett and Charlie def growProtein(self): self.delcrea() cmd.mstop() cmd.mclear() cmd.mset() self.update(self.p) objects = cmd.get_names('all') self.checkitforthese() if 'protein' in objects: self.set_defaults() cmd.bg_color('black') # create the objects to be used in this movie cmd.create('helix', 'ss h and protein') cmd.create('sheets', 'ss s and protein') cmd.create('surface', objects[0]) cmd.mset('1', '1400') # dna and rna will be represented as sticks # to make them stand out from the protein if 'dna' in objects: cmd.show('sticks','dna') self.cpknucleic() if 'rna' in objects: cmd.show('sticks','rna') cmd.show('spheres','rna') cmd.set('sphere_scale','0.4','rna') self.color_cpk(' & rna') # coloring the protein and secondary structures cmd.color('white', 'protein') cmd.color('purple', 'helix') cmd.color('teal', 'sheets') cmd.cartoon('loop', 'protein') cmd.cartoon('automatic', 'helix') cmd.cartoon('automatic', 'sheets') cmd.show('cartoon', 'protein') #cmd.do('mdo 1: hide cartoon, helix; hide cartoon, sheets;') cmd.util.mrock('2','200','90','1','1') cmd.do('mdo 201: show cartoon, helix;') cmd.util.mrock('202','400','90','1','1') cmd.do('mdo 401: show cartoon, sheets;') cmd.util.mrock('402','600','90','1','1') if 'ligands' in objects: cmd.color('hotpink','ligands') cmd.do('mdo 600: show spheres, ligands; show sticks, ligands; set sphere_transparency=0.5, ligands;') cmd.util.mroll('601','800','1',axis="x") cmd.color('blue', 'surface') cmd.mview('store', '800') cmd.do('turn z, 180') cmd.mview('store' ,'1000') cmd.do('turn z, 180') cmd.do('mdo 800: show surface, surface; set transparency=0.8, surface;') cmd.do('mdo 850: set transparency=0.7, surface;') cmd.do('mdo 900: set transparency=0.6, surface;') cmd.do('mdo 950: set transparency=0.5, surface;') cmd.do('mdo 1000: set transparency=0.4, surface;') cmd.do('mdo 1050: set transparency=0.3, surface;') cmd.do('mdo 1100: set transparency=0.2, surface;') cmd.do('mdo 1150: set transparency=0.1, surface;') cmd.do('mdo 1200: set transparency=0.0, surface;') cmd.mview('store', '1200') cmd.util.mrock('1201','1399','180','1','1') cmd.hide('everything', 'surface') cmd.hide('everything', 'helix') cmd.hide('everything', 'sheets') cmd.reset() cmd.orient() cmd.do('mdo 1400: hide everything, all; show cartoon, protein;') cmd.do('mdo 1400: mstop') cmd.mview('interpolate') cmd.rewind() #---------Version 2--------# #--------Haven't you seeen my MOVIES!----------- #surface over cartoon movie def surface_cartoon(self): self.delcrea() self.update(self.p) cmd.mstop() cmd.mclear() cmd.mset() cmd.mset('1','60') cmd.hide('everything') objects = cmd.get_names('all') cmd.create('surface','all') cmd.create('cartoon','all') cmd.show('cartoon', 'cartoon') cmd.show('surface', 'surface') cmd.color('grey', 'surface') cmd.color('red', 'elem O') cmd.color('blue', 'elem N') cmd.set("cartoon_fancy_helices", "1") cmd.set("cartoon_fancy_sheets", "1") cmd.do('mdo 1: set transparency=0.75, surface;') cmd.do('mdo 2: set transparency=0.7, surface;') cmd.do('mdo 3: set transparency=0.65, surface;') cmd.do('mdo 4: set transparency=0.6, surface;') cmd.do('mdo 5: set transparency=0.55, surface;') cmd.do('mdo 6: set transparency=0.5, surface;') cmd.do('mdo 7: set transparency=0.45, surface;') cmd.do('mdo 8: set transparency=0.4, surface;') cmd.do('mdo 9: set transparency=0.35, surface;') cmd.do('mdo 10: set transparency=0.3, surface;') cmd.do('mdo 11: set transparency=0.25, surface;') cmd.do('mdo 12: set transparency=0.2, surface;') cmd.do('mdo 13: set transparency=0.15, surface;') cmd.do('mdo 14: set transparency=0.1, surface;') cmd.do('mdo 15: set transparency=0.05, surface;') cmd.do('mdo 16: set transparency=0, surface;') cmd.do('mdo 17: set transparency=0, surface;') cmd.do('mdo 19: set transparency=0, surface;') cmd.do('mdo 20: set transparency=0, surface;') cmd.do('mdo 21: set transparency=0, surface;') cmd.do('mdo 22: set transparency=0, surface;') cmd.do('mdo 23: set transparency=0, surface;') cmd.do('mdo 24: set transparency=0, surface;') cmd.do('mdo 25: set transparency=0, surface;') cmd.do('mdo 26: set transparency=0, surface;') cmd.do('mdo 27: set transparency=0, surface;') cmd.do('mdo 28: set transparency=0, surface;') cmd.do('mdo 29: set transparency=0.05, surface;') cmd.do('mdo 30: set transparency=0.1, surface;') cmd.do('mdo 31: set transparency=0.15, surface;') cmd.do('mdo 32: set transparency=0.2, surface;') cmd.do('mdo 33: set transparency=0.25, surface;') cmd.do('mdo 34: set transparency=0.3, surface;') cmd.do('mdo 35: set transparency=0.35, surface;') cmd.do('mdo 36: set transparency=0.4, surface;') cmd.do('mdo 37: set transparency=0.45, surface;') cmd.do('mdo 38: set transparency=0.5, surface;') cmd.do('mdo 39: set transparency=0.55, surface;') cmd.do('mdo 40: set transparency=0.6, surface;') cmd.do('mdo 41: set transparency=0.65, surface;') cmd.do('mdo 42: set transparency=0.7, surface;') cmd.do('mdo 43: set transparency=0.75, surface;') cmd.do('mdo 44: set transparency=0.8, surface;') cmd.do('mdo 45: set transparency=0.85, surface;') cmd.do('mdo 46: set transparency=0.9, surface;') cmd.do('mdo 47: set transparency=0.9, surface;') cmd.do('mdo 48: set transparency=0.9, surface;') cmd.do('mdo 49: set transparency=0.85, surface;') cmd.do('mdo 50: set transparency=0.85, surface;') cmd.do('mdo 51: set transparency=0.85, surface;') cmd.do('mdo 52: set transparency=0.85, surface;') cmd.do('mdo 53: set transparency=0.85, surface;') cmd.do('mdo 54: set transparency=0.85, surface;') cmd.do('mdo 55: set transparency=0.85, surface;') cmd.do('mdo 56: set transparency=0.85, surface;') cmd.do('mdo 57: set transparency=0.85, surface;') cmd.do('mdo 58: set transparency=0.85, surface;') cmd.do('mdo 59: set transparency=0.85, surface;') cmd.do('mdo 60: set transparency=0.8, surface;') #surface over stick movie def surface_stick(self): self.delcrea() self.update(self.p) cmd.mstop() cmd.mclear() cmd.mset('1','60') cmd.hide('everything') objects = cmd.get_names('all') cmd.create('surface', 'all') cmd.create('sticks', 'all') cmd.show('sticks', 'sticks') self.color_cpk('& sticks') cmd.show('surface', 'surface') cmd.color('grey', 'surface') cmd.color('red', 'elem O') cmd.color('blue', 'elem N') cmd.do('mdo 1: set transparency=0.75, surface;') cmd.do('mdo 2: set transparency=0.7, surface;') cmd.do('mdo 3: set transparency=0.65, surface;') cmd.do('mdo 4: set transparency=0.6, surface;') cmd.do('mdo 5: set transparency=0.55, surface;') cmd.do('mdo 6: set transparency=0.5, surface;') cmd.do('mdo 7: set transparency=0.45, surface;') cmd.do('mdo 8: set transparency=0.4, surface;') cmd.do('mdo 9: set transparency=0.35, surface;') cmd.do('mdo 10: set transparency=0.3, surface;') cmd.do('mdo 11: set transparency=0.25, surface;') cmd.do('mdo 12: set transparency=0.2, surface;') cmd.do('mdo 13: set transparency=0.15, surface;') cmd.do('mdo 14: set transparency=0.1, surface;') cmd.do('mdo 15: set transparency=0.05, surface;') cmd.do('mdo 16: set transparency=0, surface;') cmd.do('mdo 17: set transparency=0, surface;') cmd.do('mdo 19: set transparency=0, surface;') cmd.do('mdo 20: set transparency=0, surface;') cmd.do('mdo 21: set transparency=0, surface;') cmd.do('mdo 22: set transparency=0, surface;') cmd.do('mdo 23: set transparency=0, surface;') cmd.do('mdo 24: set transparency=0, surface;') cmd.do('mdo 25: set transparency=0, surface;') cmd.do('mdo 26: set transparency=0, surface;') cmd.do('mdo 27: set transparency=0, surface;') cmd.do('mdo 28: set transparency=0, surface;') cmd.do('mdo 29: set transparency=0.05, surface;') cmd.do('mdo 30: set transparency=0.1, surface;') cmd.do('mdo 31: set transparency=0.15, surface;') cmd.do('mdo 32: set transparency=0.2, surface;') cmd.do('mdo 33: set transparency=0.25, surface;') cmd.do('mdo 34: set transparency=0.3, surface;') cmd.do('mdo 35: set transparency=0.35, surface;') cmd.do('mdo 36: set transparency=0.4, surface;') cmd.do('mdo 37: set transparency=0.45, surface;') cmd.do('mdo 38: set transparency=0.5, surface;') cmd.do('mdo 39: set transparency=0.55, surface;') cmd.do('mdo 40: set transparency=0.6, surface;') cmd.do('mdo 41: set transparency=0.65, surface;') cmd.do('mdo 42: set transparency=0.7, surface;') cmd.do('mdo 43: set transparency=0.75, surface;') cmd.do('mdo 44: set transparency=0.8, surface;') cmd.do('mdo 45: set transparency=0.85, surface;') cmd.do('mdo 46: set transparency=0.9, surface;') cmd.do('mdo 47: set transparency=0.9, surface;') cmd.do('mdo 48: set transparency=0.9, surface;') cmd.do('mdo 49: set transparency=0.85, surface;') cmd.do('mdo 50: set transparency=0.85, surface;') cmd.do('mdo 51: set transparency=0.85, surface;') cmd.do('mdo 52: set transparency=0.85, surface;') cmd.do('mdo 53: set transparency=0.85, surface;') cmd.do('mdo 54: set transparency=0.85, surface;') cmd.do('mdo 55: set transparency=0.85, surface;') cmd.do('mdo 56: set transparency=0.85, surface;') cmd.do('mdo 57: set transparency=0.85, surface;') cmd.do('mdo 58: set transparency=0.85, surface;') cmd.do('mdo 59: set transparency=0.85, surface;') cmd.do('mdo 60: set transparency=0.8, surface;') #movie that pulls ligands out of and puts them back in def Ligand_Pull(self): self.delcrea() self.update(self.p) cmd.mstop() cmd.mclear() cmd.mset('1','442') cmd.hide('everything') cmd.remove('resn HOH') cmd.color('green', 'all') objects = cmd.get_names('all') cmd.select("Bad", "resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR+ACD+ACE+ALB+ALI+ABU+ARO+ASX+BAS+BET+FOR+GLX+HET+HSE+HYP+HYL+ORN+PCA+SAR+TAU+TER+THY+UNK+a+g+c+t+u+HOH+MSE") cmd.select("ligand","!Bad") cmd.hide("everything", "ligand") cmd.show("spheres", "ligand") cmd.show("sticks", "ligand around 6'") cmd.set('stick_radius','0.3','ligand around 6') cmd.color('orange', 'ligand') cmd.select("interaction","ligand around 6'") self.cpkinteraction() cmd.delete('interaction') cmd.delete("Bad") cmd.show('cartoon', "resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR+ACD+ACE+ALB+ALI+ABU+ARO+ASX+BAS+BET+FOR+GLX+HET+HSE+HYP+HYL+ORN+PCA+SAR+TAU+TER+THY+UNK+a+g+c+t+u+HOH+MSE") cmd.set("cartoon_fancy_helices", "1") cmd.set("cartoon_fancy_sheets", "1") cmd.set('cartoon_transparency','0.5') cmd.zoom() cmd.orient() cmd.do('mdo 1: orient') cmd.do('mdo 2: translate [2,0,0],ligand;') cmd.do('mdo 3: translate [2,0,0],ligand;') cmd.do('mdo 4: translate [2,0,0],ligand;') cmd.do('mdo 5: translate [2,0,0],ligand;') cmd.do('mdo 6: translate [2,0,0],ligand;') cmd.do('mdo 7: translate [2,0,0],ligand;') cmd.do('mdo 8: translate [2,0,0],ligand;') cmd.do('mdo 9: translate [2,0,0],ligand;') cmd.do('mdo 10: translate [2,0,0],ligand;') cmd.do('mdo 11: translate [2,0,0],ligand;') cmd.do('mdo 12: translate [2,0,0],ligand;') cmd.do('mdo 13: translate [2,0,0],ligand;') cmd.do('mdo 14: translate [2,0,0],ligand;') cmd.do('mdo 15: translate [2,0,0],ligand;') cmd.do('mdo 16: translate [2,0,0],ligand;') cmd.do('mdo 17: translate [2,0,0],ligand;') cmd.do('mdo 18: translate [2,0,0],ligand;') cmd.do('mdo 19: translate [2,0,0],ligand;') cmd.do('mdo 20: translate [2,0,0],ligand;') cmd.do('mdo 21: translate [2,0,0],ligand;') cmd.do('mdo 22: translate [2,0,0],ligand;') cmd.do('mdo 23: translate [2,0,0],ligand;') cmd.do('mdo 24: translate [2,0,0],ligand;') cmd.do('mdo 25: translate [2,0,0],ligand;') cmd.do('mdo 26: translate [2,0,0],ligand;') cmd.do('mdo 27: translate [2,0,0],ligand;') cmd.do('mdo 28: translate [2,0,0],ligand;') cmd.do('mdo 29: translate [2,0,0],ligand;') cmd.do('mdo 30: translate [2,0,0],ligand;') cmd.do('mdo 31: translate [2,0,0],ligand;') cmd.do('mdo 32: translate [2,0,0],ligand;') cmd.do('mdo 33: translate [2,0,0],ligand;') cmd.do('mdo 34: translate [2,0,0],ligand;') cmd.do('mdo 35: translate [2,0,0],ligand;') cmd.do('mdo 36: translate [2,0,0],ligand;') cmd.do('mdo 37: translate [2,0,0],ligand;') cmd.do('mdo 38: translate [2,0,0],ligand;') cmd.do('mdo 39: translate [2,0,0],ligand;') cmd.do('mdo 40: translate [2,0,0],ligand;') cmd.do('mdo 41: translate [2,0,0],ligand;') cmd.do('mdo 42: orient') cmd.util.mroll('42','222','1') cmd.do('mdo 223: translate [-2,0,0],ligand;') cmd.do('mdo 224: translate [-2,0,0],ligand;') cmd.do('mdo 225: translate [-2,0,0],ligand;') cmd.do('mdo 226: translate [-2,0,0],ligand;') cmd.do('mdo 227: translate [-2,0,0],ligand;') cmd.do('mdo 228: translate [-2,0,0],ligand;') cmd.do('mdo 229: translate [-2,0,0],ligand;') cmd.do('mdo 230: translate [-2,0,0],ligand;') cmd.do('mdo 231: translate [-2,0,0],ligand;') cmd.do('mdo 232: translate [-2,0,0],ligand;') cmd.do('mdo 233: translate [-2,0,0],ligand;') cmd.do('mdo 234: translate [-2,0,0],ligand;') cmd.do('mdo 235: translate [-2,0,0],ligand;') cmd.do('mdo 236: translate [-2,0,0],ligand;') cmd.do('mdo 237: translate [-2,0,0],ligand;') cmd.do('mdo 238: translate [-2,0,0],ligand;') cmd.do('mdo 239: translate [-2,0,0],ligand;') cmd.do('mdo 240: translate [-2,0,0],ligand;') cmd.do('mdo 241: translate [-2,0,0],ligand;') cmd.do('mdo 242: translate [-2,0,0],ligand;') cmd.do('mdo 243: translate [-2,0,0],ligand;') cmd.do('mdo 244: translate [-2,0,0],ligand;') cmd.do('mdo 245: translate [-2,0,0],ligand;') cmd.do('mdo 246: translate [-2,0,0],ligand;') cmd.do('mdo 247: translate [-2,0,0],ligand;') cmd.do('mdo 248: translate [-2,0,0],ligand;') cmd.do('mdo 249: translate [-2,0,0],ligand;') cmd.do('mdo 250: translate [-2,0,0],ligand;') cmd.do('mdo 251: translate [-2,0,0],ligand;') cmd.do('mdo 252: translate [-2,0,0],ligand;') cmd.do('mdo 253: translate [-2,0,0],ligand;') cmd.do('mdo 254: translate [-2,0,0],ligand;') cmd.do('mdo 255: translate [-2,0,0],ligand;') cmd.do('mdo 256: translate [-2,0,0],ligand;') cmd.do('mdo 257: translate [-2,0,0],ligand;') cmd.do('mdo 258: translate [-2,0,0],ligand;') cmd.do('mdo 259: translate [-2,0,0],ligand;') cmd.do('mdo 260: translate [-2,0,0],ligand;') cmd.do('mdo 261: translate [-2,0,0],ligand;') cmd.do('mdo 262: translate [-2,0,0],ligand;') cmd.do('mdo 263: orient') cmd.util.mroll('264','442','1') #movie that pulls protein chains apart and shows interaction, then puts them together again def chain_pull(self): self.delcrea() self.update(self.p) cmd.mstop() cmd.mclear() cmd.mset('1', '373') cmd.hide('everything') cmd.show('mesh', 'all') cmd.color('gray40', 'all') cmd.select("Chain-A", "chain A") cmd.select("Chain-B", "chain B") cmd.select("Chain-C", "chain C") cmd.select("Chain-D", "chain D") cmd.select("Chain-E", "chain E") cmd.select("Chain-F", "chain F") cmd.select("Chain-G", "chain G") cmd.select("Chain-H", "chain H") cmd.select("Chain-I", "chain I") cmd.select("Chain-J", "chain J") cmd.select("Chain-K", "chain K") cmd.select("Chain-L", "chain L") cmd.select("Chain-M", "chain M") cmd.select("Chain-N", "chain N") cmd.select("Chain-O", "chain O") cmd.select("Chain-P", "chain P") cmd.select("Chain-Q", "chain Q") cmd.select("Chain-R", "chain R") cmd.select("Chain-S", "chain S") cmd.select("Chain-T", "chain T") cmd.select("Chain-U", "chain U") cmd.select("Chain-V", "chain V") cmd.select("Chain-W", "chain W") cmd.select("Chain-X", "chain X") cmd.select("Chain-Y", "chain Y") cmd.select("Chain-Z", "chain Z") self.checkforchain() cmd.orient() objects = cmd.get_names('all') chainpulllist = [] if 'Chain-A' in objects: chainpulllist.append('Chain-A') if 'Chain-B' in objects: chainpulllist.append('Chain-B') if 'Chain-C' in objects: chainpulllist.append('Chain-C') if 'Chain-D' in objects: chainpulllist.append('Chain-D') if 'Chain-E' in objects: chainpulllist.append('Chain-E') if 'Chain-F' in objects: chainpulllist.append('Chain-F') if 'Chain-G' in objects: chainpulllist.append('Chain-G') if 'Chain-H' in objects: chainpulllist.append('Chain-H') if 'Chain-I' in objects: chainpulllist.append('Chain-I') if 'Chain-J' in objects: chainpulllist.append('Chain-J') if 'Chain-K' in objects: chainpulllist.append('Chain-K') if 'Chain-L' in objects: chainpulllist.append('Chain-L') if 'Chain-M' in objects: chainpulllist.append('Chain-M') if 'Chain-N' in objects: chainpulllist.append('Chain-N') if 'Chain-O' in objects: chainpulllist.append('Chain-O') if 'Chain-P' in objects: chainpulllist.append('Chain-P') if 'Chain-Q' in objects: chainpulllist.append('Chain-Q') if 'Chain-R' in objects: chainpulllist.append('Chain-R') if 'Chain-S' in objects: chainpulllist.append('Chain-S') if 'Chain-T' in objects: chainpulllist.append('Chain-T') if 'Chain-U' in objects: chainpulllist.append('Chain-U') if 'Chain-V' in objects: chainpulllist.append('Chain-V') if 'Chain-W' in objects: chainpulllist.append('Chain-W') if 'Chain-X' in objects: chainpulllist.append('Chain-X') if 'Chain-Y' in objects: chainpulllist.append('Chain-Y') if 'Chain-Z' in objects: chainpulllist.append('Chain-Z') if len(chainpulllist) >1: cmd.do('mdo 2: translate [0,0,0],'+chainpulllist[0]+';') cmd.do('mdo 3: translate [50,0,0],'+chainpulllist[1]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >2: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[1]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[1] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >2: cmd.do('mdo 4: translate [0,50,0],'+chainpulllist[2]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[2]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[2] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >3: cmd.do('mdo 5: translate [0,0,50],'+chainpulllist[3]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[3]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[3] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >4: cmd.do('mdo 6: translate [-50,0,0],'+chainpulllist[4]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[4]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[4] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >5: cmd.do('mdo 7: translate [0,-50,0],'+chainpulllist[5]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[5]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[5] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >6: cmd.do('mdo 8: translate [0,-50,0],'+chainpulllist[5]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[6]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[6] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >7: cmd.do('mdo 9: translate [0,0,-50],'+chainpulllist[6]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[7]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[7] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >8: cmd.do('mdo 10: translate [-50,0,50],'+chainpulllist[7]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[8]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[8] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >9: cmd.do('mdo 11: translate [50,0,50],'+chainpulllist[8]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[9]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[9] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') if len(chainpulllist) >10: cmd.do('mdo 12: translate [50,0,-50],'+chainpulllist[10]+';') cmd.do('select duh,' +chainpulllist[0] + ' within 5 of ' + chainpulllist[10]) self.cpkduh() cmd.delete('duh') cmd.do('select duh,' +chainpulllist[10] + ' within 5 of ' + chainpulllist[0]) self.cpkduh() cmd.delete('duh') cmd.do('mdo 13: zoom all') cmd.util.mroll('14','181','1') if len(chainpulllist) >1: cmd.do('mdo 183: translate [0,0,0],'+chainpulllist[0]+';') cmd.do('mdo 184: translate [-50,0,0],'+chainpulllist[1]+';') cmd.zoom() if len(chainpulllist) >2: cmd.do('mdo 185: translate [0,-50,0],'+chainpulllist[2]+';') cmd.zoom() if len(chainpulllist) >3: cmd.do('mdo 186: translate [0,0,-50],'+chainpulllist[3]+';') cmd.zoom() if len(chainpulllist) >4: cmd.do('mdo 187: translate [50,0,0],'+chainpulllist[4]+';') cmd.zoom() if len(chainpulllist) >5: cmd.do('mdo 188: translate [0,50,0],'+chainpulllist[5]+';') cmd.zoom() if len(chainpulllist) >6: cmd.do('mdo 189: translate [0,0,50],'+chainpulllist[6]+';') cmd.zoom() if len(chainpulllist) >7: cmd.do('mdo 190: translate [50,0,-50],'+chainpulllist[7]+';') cmd.zoom() if len(chainpulllist) >8: cmd.do('mdo 191: translate [-50,0,-50],'+chainpulllist[8]+';') cmd.zoom() if len(chainpulllist) >9: cmd.do('mdo 192: translate [50,0,50],'+chainpulllist[9]+';') cmd.zoom() if len(chainpulllist) >10: cmd.do('mdo 193: translate [-50,0,50],'+chainpulllist[10]+';') cmd.do('mdo 194: zoom all') cmd.util.mroll('195','373','1') #movie controls def play(self): cmd.mplay() def stop(self): cmd.mstop() def rewind(self): cmd.mstop() cmd.rewind() #Ray Trace Frames def ray(self,r,state): import tkMessageBox if state: if tkMessageBox.askyesno('Ray Trace Frames', 'Enabling this feature may '+ 'slow own the playback of your movie significantly. '+ 'Are you sure that you want to proceed?'): cmd.set('ray_trace_frames','1') else: self.ray.invoke('Ray Trace Frames') else: cmd.set('ray_trace_frames','0') def cacheframe(self,r,state): if state: cmd.set('cache_frames','0') else: cmd.set('cache_frames', '1') # Copyright Notice # ================ # # The PyMOL Plugin source code in this file is copyrighted, but you can # freely use and copy it as long as you don't change or remove any of # the copyright notices. # # ---------------------------------------------------------------------- # This PyMOL Plugin is Copyright (C) 2004 by Charles Moad # # All Rights Reserved # # Permission to use, copy, modify, distribute, and distribute modified # versions of this software and its documentation for any purpose and # without fee is hereby granted, provided that the above copyright # notice appear in all copies and that both the copyright notice and # this permission notice appear in supporting documentation, and that # the name(s) of the author(s) not be used in advertising or publicity # pertaining to distribution of the software without specific, written # prior permission. # # THE AUTHOR(S) DISCLAIM ALL WARRANTIES WITH REGARD TO THIS SOFTWARE, # INCLUDING ALL IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS. IN # NO EVENT SHALL THE AUTHOR(S) BE LIABLE FOR ANY SPECIAL, INDIRECT OR # CONSEQUENTIAL DAMAGES OR ANY DAMAGES WHATSOEVER RESULTING FROM LOSS OF # USE, DATA OR PROFITS, WHETHER IN AN ACTION OF CONTRACT, NEGLIGENCE OR # OTHER TORTIOUS ACTION, ARISING OUT OF OR IN CONNECTION WITH THE USE OR # PERFORMANCE OF THIS SOFTWARE. # ---------------------------------------------------------------------- def getPdb(self): import tkSimpleDialog import tkMessageBox import urllib import gzip import os import string if self.fileLoaded ==' ': pdbCode = tkSimpleDialog.askstring('PDB Loader Service', 'Please enter a 4-digit pdb code:') else: pdbCode=self.fileLoaded #print pdbCode if pdbCode: # None is returned for user cancel pdbCode = string.upper(pdbCode) filename = urllib.urlretrieve('http://www.rcsb.org/pdb/cgi/export.cgi/' + pdbCode + '.pdb.gz?format=PDB&pdbId=' + pdbCode + '&compression=gz')[0] # If 0, then pdb code was invalid if (os.path.getsize(filename) > 0): # Decompress the file while reading fpin = gzip.open(filename) # Form the pdb output name outputname = os.path.dirname(filename) + os.sep + pdbCode + '.pdb' fpout = open(outputname, 'w') fpout.write(fpin.read()) # Write pdb file fpin.close() fpout.close() cmd.load(outputname) # Load the fresh pdb #---------------THIS WAS JUST ADDED--------------------------- self.p=PDBParser() self.p.readFile(outputname) self.update(self.p) cmd.deselect() else: tkMessageBox.showerror('Invalid Code', 'You entered an invalid pdb code:' + pdbCode) os.remove(filename) # Remove tmp file (leave the pdb) #------Open Help File---------# def help(self): import webbrowser try: webbrowser.open('./modules/pmg_tk/startup/Help/EZ-Viz.chm') except: webbrowser.open('./modules/pmg_tk/startup/Help/EZ-VizWebMain.html') #---------------------------------------------------------------# # # # GUI CREATION METHOD # # (INIT) # # # # # # create and organize the interface # # # #---------------------------------------------------------------# def __init__(self, app): self.pdbCode = ' ' self.p=PDBParser() self.converter = ChimeConverter() # initialize the additional colors self.init_color() self.sel1='all' # create the dialog box which contains the GUI parent = app.root self.dialog = Pmw.Dialog(parent,buttons = ('Open','Fetch PDB','Clear','Help', 'Thanks' ,'Quit'), title = 'Pro-MOL',command = self.execute) # set the size of the #self.dialog.geometry('550x550') interior = self.dialog.interior() #TITLE BAR lab = Label(interior, text='ProMol\nDeveloped By: Charlie Westin, Brett Hanson & Paul Craig\nVersion 3.02, 2007', background='#000066', foreground='white') lab.pack(expand=0, fill='x', padx=4, pady=0) # Create the notebook to hold the tabs notebook = Pmw.NoteBook(interior) notebook.pack(fill='both', expand=1, padx=10, pady=10) #--------------------------------------# # # # WELCOME TAB # # # #--------------------------------------# page = notebook.add('Welcome') notebook.tab('Welcome').focus_set() canvas=Canvas(page) canvas.pack(fill='both', expand=1) canvas.create_image(0,0,image=splash,anchor=NW) #-------------Version 2----------------# #----------------------------------------# # # # EZ-Viz TAB # # # #--------------------------------------# # Add "Settings" tab to notebook page = notebook.add('EZ-Viz') #------Wirte Script Out------------- self.scriptwrite = Pmw.OptionMenu(page,label_text = 'Script Writing:',labelpos = 'n', items = ("Off", "On"), menubutton_width = 11, command=self.write_script) self.scriptwrite.grid(row=5,column=0,sticky=NW) group = Pmw.Group(page, tag_text='Run Script') group.grid(row=5, column=0, padx=8, pady=0, sticky = N) interior = group.interior() scriptbutton = Button(interior, width = 10, text = 'Run Script') scriptbutton.grid() loaderent = Entry(interior, width = 7) def loadlog(event): loaderent.delete(0, 1000) import tkFileDialog file = tkFileDialog.askopenfilename(defaultextension=".pml") loaderent.insert(0, file) cmd.do('@'+loaderent.get()) page.mainloop() scriptbutton.bind('', loadlog) #------------ Presets Group --------------- group = Pmw.Group(page, tag_text='Preset Views') group.grid(row=0, column=0, padx=0, pady=0) interior=group.interior() #menus for presets surface = Pmw.OptionMenu(interior,label_text = 'Surfaces:',labelpos = 'n', items = ('','Surface','Surface on Cartoon','Surface on Sticks', 'Surface on Spheres', 'Mesh on Sticks', 'Dots on Lines'), menubutton_width = 10, command=self.presurf) surface.grid(row=0,column=0,sticky=NW) cartoon = Pmw.OptionMenu(interior,label_text = 'Cartoons:',labelpos = 'n', items = ('','Cartoon','Putty','Lines on Cartoon', 'Color by Chain'), menubutton_width = 10, command=self.pretoon) cartoon.grid(row=0,column=1,sticky=NW) residue = Pmw.OptionMenu(interior,label_text = 'By Residue:',labelpos = 'n', items = ('','Aromatics','Show Charged','Solubility'), menubutton_width = 10, command=self.preres) residue.grid(row=0,column=2,sticky=NW) roving = Pmw.OptionMenu(interior,label_text = 'Roving:',labelpos = 'n', items = ('','Roving Sticks','Roving Ball&Sticks','Roving Spheres', 'Roving Lines'), menubutton_width = 10, command=self.prerov) roving.grid(row=1,column=2,sticky=NW) elecdensity = Pmw.OptionMenu(interior,label_text = 'Electron Density:',labelpos = 'n', items = ('','Mesh on Ribbon','Dots on Sticks','Surface on Lines'), menubutton_width = 10, command=self.preele) elecdensity.grid(row=1,column=1,sticky=NW) misc = Pmw.OptionMenu(interior,label_text = 'Miscellaneous:',labelpos = 'n', items = ('','Hetero Atoms','Chain Contacts','DNA & RNA','CPK','Ball & Stick'), menubutton_width = 10, command=self.premisc) misc.grid(row=1,column=0,sticky=NW) #roving slider self.rovingradius2 = Scale(interior, width =8) self.rovingradius2.configure(showvalue="0") self.rovingradius2.configure(troughcolor="#ffffff") self.rovingradius2.configure(length="90") self.rovingradius2.configure(orient="horizontal") self.rovingradius2.configure(resolution="0.1") self.rovingradius2.configure(to="15.0") self.rovingradius2.grid(row=1, column=3, padx=0, pady=0, sticky=S) self.rovingradius2.set(8.0) labelradius = Label(interior, text = 'Roving Detail') labelradius.grid(row=1, column=3, padx=0, pady=0, sticky=N) #preset movies dropdown movies = Pmw.OptionMenu(interior,label_text = 'Preset Movies:',labelpos = 'n', items = ('','Ligand Zoom','Build Protein','Highlight Chains','Rotate','Chain Pull', 'Ligand Pull', 'Surface to Stick', 'Surface to Cartoon', 'Play', 'Stop', 'Rewind'), menubutton_width = 10, command=self.premovie) movies.grid(row=0,column=3,sticky=NW) #---------------Version 1-----------------# #------------ Display Group ----------------# # # # # #-------------------------------------------# group = Pmw.Group(page, tag_text='Display Options') group.grid(row=4, column=0, columnspan=2, padx=0, pady=0) self.int=group.interior() # menu for stereo options stereo = Pmw.OptionMenu(self.int,label_text = 'Stereo:',labelpos = 'n', items = ("Off", "Quad", "Cross-Eye", "Wall-Eye"), menubutton_width = 11, command=self.stereo_switch) stereo.grid(row=0,column=0,sticky=NW) # menu for background color changes stereo = Pmw.OptionMenu(self.int,label_text = 'Background Color:',labelpos = 'n', items = ("Black", "White", "Grey", "Other"), menubutton_width = 11, command=self.bgcolor_switch) stereo.grid(row=0,column=1,sticky=NW) # menu for background color changes stereo = Pmw.OptionMenu(self.int,label_text = 'Color Space:',labelpos = 'n', items = ("PyMOL", "Publications", "Video/Web"), menubutton_width = 11, command=self.cspace_switch) stereo.grid(row=0,column=2,sticky=NW) # menu for hide/show interface stereo = Pmw.OptionMenu(self.int,label_text = 'Internal GUI:',labelpos = 'n', items = ("Show", "Hide"), menubutton_width = 11, command=self.hide_interface) stereo.grid(row=0,column=3,sticky=NW) #----------------Version 2------------# # AUTOMATED COMMANDS TAB group = Pmw.Group(page, tag_text = 'Automated Commands') group.grid(row=2, column=0, padx=0, pady=0) interior = group.interior() def populater(event): objects = cmd.get_names('all') cmd.select('protein','resn GLY+PRO+ALA+VAL+LEU+ILE+MET+CYS+PHE+TYR+TRP+HIS+LYS+ARG+GLN+ASN+GLU+ASP+SER+THR') cmd.select('nucleic_acid', 'resn a+t+g+c+u') cmd.select('hydrophobic','resn ALA+ILE+LEU+MET+PHE+PRO+TRP+VAL') cmd.select('hydrophilic','resn THR+SER+ARG+ASN+ASP+GLN+GLU+HIS+LYS') cmd.select('acidic','resn ASP+GLU') cmd.select('basic','resn ARG+HIS+LYS') cmd.select('ligands', 'het') cmd.select('heme', 'resn hem') cmd.disable('heme') cmd.disable('ligands') cmd.disable('basic') cmd.disable('acidic') cmd.disable('hydrophilic') cmd.disable('hydrophobic') cmd.disable('nucleic_acid') cmd.disable('protein') self.checkitforthese() cmd.select("Chain-A", "chain A") cmd.select("Chain-B", "chain B") cmd.select("Chain-C", "chain C") cmd.select("Chain-D", "chain D") cmd.select("Chain-E", "chain E") cmd.select("Chain-F", "chain F") cmd.select("Chain-G", "chain G") cmd.select("Chain-H", "chain H") cmd.select("Chain-I", "chain I") cmd.select("Chain-J", "chain J") cmd.select("Chain-K", "chain K") cmd.select("Chain-L", "chain L") cmd.select("Chain-M", "chain M") cmd.select("Chain-N", "chain N") cmd.select("Chain-O", "chain O") cmd.select("Chain-P", "chain P") cmd.select("Chain-Q", "chain Q") cmd.select("Chain-R", "chain R") cmd.select("Chain-S", "chain S") cmd.select("Chain-T", "chain T") cmd.select("Chain-U", "chain U") cmd.select("Chain-V", "chain V") cmd.select("Chain-W", "chain W") cmd.select("Chain-X", "chain X") cmd.select("Chain-Y", "chain Y") cmd.select("Chain-Z", "chain Z") self.checkforchain() items=[] objects = cmd.get_names('all') items.append('All') items.append('Not Selected') if 'protein' in objects: items.append('protein') if 'nucleic_acid' in objects: items.append('nucleic_acid') if 'hydrophobic' in objects: items.append('hydrophobic') if 'hydrophilic' in objects: items.append('hydrophilic') if 'acidic' in objects: items.append('acidic') if 'basic' in objects: items.append('basic') if 'ligands' in objects: items.append('ligands') if 'heme' in objects: items.append('heme') if 'Chain-A' in objects: items.append('Chain-A') if 'Chain-B' in objects: items.append('Chain-B') if 'Chain-C' in objects: items.append('Chain-C') if 'Chain-D' in objects: items.append('Chain-D') if 'Chain-E' in objects: items.append('Chain-E') if 'Chain-F' in objects: items.append('Chain-F') if 'Chain-G' in objects: items.append('Chain-G') if 'Chain-H' in objects: items.append('Chain-H') if 'Chain-I' in objects: items.append('Chain-I') if 'Chain-J' in objects: items.append('Chain-J') if 'Chain-K' in objects: items.append('Chain-K') if 'Chain-L' in objects: items.append('Chain-L') if 'Chain-M' in objects: items.append('Chain-M') if 'Chain-N' in objects: items.append('Chain-N') if 'Chain-O' in objects: items.append('Chain-O') if 'Chain-P' in objects: items.append('Chain-P') if 'Chain-Q' in objects: items.append('Chain-Q') if 'Chain-R' in objects: items.append('Chain-R') if 'Chain-S' in objects: items.append('Chain-S') if 'Chain-T' in objects: items.append('Chain-T') if 'Chain-U' in objects: items.append('Chain-U') if 'Chain-V' in objects: items.append('Chain-V') if 'Chain-W' in objects: items.append('Chain-W') if 'Chain-X' in objects: items.append('Chain-X') if 'Chain-Y' in objects: items.append('Chain-Y') if 'Chain-Z' in objects: items.append('Chain-Z') items.sort() self.selection.setitems(items) self.advancedSelection.setitems(items) self.sel = 'All' self.sel1 = 'All' popbtn=Button(interior, text='Update Selection',width=15) popbtn.place(x=50, y=32) popbtn.bind('', populater) #-------------Version 1---------------# self.selection = Pmw.OptionMenu(interior,labelpos = 'w', label_text = 'Select:', items = (''), menubutton_width = 10, command = self.set_sel) self.selection.grid(row=0, column=0, padx=8, pady=0) self.viewOptions = Pmw.OptionMenu(interior, labelpos='w', label_text = 'Show:', items = ('Lines', 'Sticks', 'Ribbons','Cartoon','Dots','Spheres','Mesh','Surface','Ball and Stick','Water', 'Everything', 'Polar Contacts'), menubutton_width=10, command=self.show_rep) self.viewOptions.grid(row=0,column=1,padx=0,pady=0,sticky='N') self.hideOptions = Pmw.OptionMenu(interior, labelpos='w', label_text = 'Hide:', items = ('Lines', 'Sticks', 'Ribbons','Cartoon','Dots','Spheres','Mesh','Surface','Ball and Stick','Water','Everything', 'Polar Contacts'), menubutton_width=10, command=self.hide_rep) self.hideOptions.grid(row=1,column=1,padx=0,pady=0, sticky='SE') # Coloring choices selection = Pmw.OptionMenu(interior,labelpos = 'w', label_text = 'Color:', items = ('Red','Green','Blue','Orange','Violet','Yellow','CPK','Other'), menubutton_width = 7, command = self.color_sel) selection.grid(row=0, column=2, padx=0, pady=0) # MANUAL COMMANDS SECTION group = Pmw.Group(page, tag_text='Manual Commands') group.grid(row=3,column=0, padx=0,pady=0) interior = group.interior() labels = ('PyMOL','Chime') self.commandChooser = self.radioAdd(interior,'w','vertical',self.set_cmd_type,'Command Type:',labels, 0, 0, 1, 1, 'W') self.output = Pmw.ScrolledText(interior, usehullsize = 1, hull_width = 250, hull_height = 50, text_wrap= WORD) self.output.grid(row=0,column=1,padx=8,pady=2) self.output.setvalue('Command results will show in this box.\n\n') # PyMOL Command Prompt self.commandLine = Pmw.EntryField(interior, labelpos='w', label_text='Command Line:', value='Enter PyMOL Commands Here', entry_width=25, command=self.command_line) self.commandLine.grid(row=1, column=0, columnspan=2, pady=2) #---------------Version 2-------------# #--------------------------------------# # # # Motifs TAB # # # #--------------------------------------# page = notebook.add('Motifs') notebook.tab('Motifs').focus_set() #Molecular Classification Field label = Label(page, text='Protein Classification') label.grid(row=1,column=0,sticky='sw',padx=5,pady=0) self.classify = Text(page, state=NORMAL, height=1.4, width=30) self.classify.insert(END,"Protein Classification") self.classify.grid(row=2, column=0, sticky='sw',padx=5, pady=0) #Molecule Name Field self.name = StringVar() self.molName = Label(page, textvariable=self.name, font='arial, 14', wraplength='450') self.name.set("") self.molName.grid(row=0, column=0, columnspan=2,sticky='w',padx=5, pady=5) #Hetero Atoms label=Label(page, text="Hetero Atoms") label.grid(row=1, column=1, sticky='sw', padx=5, pady=0) self.het = Text(page, state=NORMAL, height=1.4, width=25) self.het.insert(END,"List of hetero atoms") self.het.grid(row=2,column=1, sticky='w',padx=5,pady=0) #mechanisim group group = Pmw.Group(page, tag_text = 'Motifs') group.grid(row=3, column=0,columnspan =2, padx=0, pady=0) interior = group.interior() # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Oxidoreductases:',labelpos = 'n', items = ('','Superoxide Dismutase','Peroxidase','Alcohol Dehydrogenase', 'Aldose Reductase','NAD Reductase', 'NAD Reductase2','Betaine aldehyde dehydrogenase'), menubutton_width = 8, command=self.oxidoreductase) stereo.grid(row=0,column=0,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Transferases:',labelpos = 'n', items = ('','Amino Transferase', 'Glutamine Amidotransferase','Thymidine Kinase', 'ACTase', 'Adenylate Kinase','SRC Family Kinase', 'Hhal Methyltransferase','Serotonin Acetyltransferase', 'Cyclin Dependent Kinase'), menubutton_width = 8, command=self.transferase) stereo.grid(row=0,column=1,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Hydrolases:',labelpos = 'n', items = ('','Serine Protease', 'Papain Like', 'Metalloprotease', 'Tyrosine Phosphatase', 'Beta Lactamase', 'O-Glycosyl', 'Cephalosporin deacetylase'), menubutton_width = 8, command=self.hydrolase) stereo.grid(row=0,column=2,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Lyases:',labelpos = 'n', items = ('','Carbonic Anhydrase', 'Carbon Carbon','Chondroitinase', 'Hyaluronate-Lyase', 'Exonuclease 3', 'Citrate Synthase'), menubutton_width = 8, command=self.lyase) stereo.grid(row=0,column=3,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Isomerases:',labelpos = 'n', items = ('','Fucose Isomerase','Triose Phosphate Isomerase', 'FK506 Cis-Trans'), menubutton_width = 8, command=self.isomerase) stereo.grid(row=1,column=0,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Ligase:',labelpos = 'n', items = (' ', 'DNA Ligase'), menubutton_width = 8, command=self.ligase) stereo.grid(row=1,column=1,sticky=NW) # Menu for motifs stereo = Pmw.OptionMenu(interior,label_text = 'Other:',labelpos = 'n', items = ('','Zinc Finger'), menubutton_width = 8, command=self.other) stereo.grid(row=1,column=2,sticky=NW) stereo = Pmw.OptionMenu(interior,label_text = 'Options:',labelpos = 'n', items = ('','Surface Pocket','Polar Contacts', 'Hide Contacts', 'Show Substrate', 'Hide Substrate', 'Show label', 'Hide Label'), menubutton_width = 8, command=self.motifoption) stereo.grid(row=1,column=3,sticky=NW) framerange = Frame(interior) framerange.grid(row=2, column=1,columnspan = 4, padx=0, pady=0, sticky=NW) ballrange = Pmw.Balloon(interior) ballrange.bind(framerange, 'Multiplier for default measured values\nRe-click on desired motif to render change') self.range = Scale(framerange, width =8) self.range.configure(troughcolor="#ffffff") self.range.configure(length="200") self.range.configure(orient="horizontal") self.range.configure(resolution="0.01") self.range.configure(to="2.0") self.range.grid(row=2, column=1,columnspan = 4, padx=0, pady=0, sticky=NW) self.range.set(1) labrange = Label(interior, text='Precision Factor:') labrange.grid(row=2, column=0, sticky=SE) self.buttonAdd(interior, 'Reset', 10, self.resetrange, 3, 3, 'SE') #---------------------Show residues around active site---------------# group = Pmw.Group(page, tag_text='Tools') group.grid(row=4, column=0, columnspan=1, padx=2, pady=2, sticky=W) interior = group.interior() framesela = Frame(interior) framesela.grid(row=0, column=0, columnspan = 2, padx=0, pady=0, sticky=N) ballsela = Pmw.Balloon(interior) ballsela.bind(framesela, 'Within # Angstroms') selA = Scale(framesela, width =8) selA.configure(troughcolor="#ffffff") selA.configure(length="130") selA.configure(orient="horizontal") selA.configure(resolution="0.2") selA.configure(to="10.0") selA.grid(row=0, column=0, columnspan= 2, padx=0, pady=0, sticky=N) selA.set(5.0) frameadj = Frame(interior) frameadj.grid(row=1, column=0, padx=1, pady=1, sticky=NW) balladj = Pmw.Balloon(interior) balladj.bind(frameadj, 'Display residues adjacent to motif') showround = Button(frameadj, width = 12, text = 'Adjacent') showround.grid(row=1, column=0, padx=1, pady=1, sticky=NW) def roundres(event): try: cmd.hide('sticks', '!'+self.mot) cmd.color('white', '!'+self.mot) cmd.select('Adjacent', 'byres '+self.mot+' around %s'%(selA.get())) cmd.show('sticks', 'Adjacent') cmd.color('orange', 'Adjacent') util.cnc('Adjacent') cmd.remove('hydro') cmd.deselect() except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must load a motif first') interior.mainloop() showround.bind('', roundres) delres = Button(interior, width = 14, text = 'Delete Adjacent') delres.grid(row=1, column=1, padx=1, pady=1, sticky=NW) def resdel(event): try: objects = cmd.get_names('all') cmd.hide('sticks', '!'+self.mot) cmd.color('white', '!'+self.mot) if 'Adjacent' in objects: cmd.delete('Adjacent_polar_conts') if 'Adjacent' in objects: cmd.label('byres Adjacent',"''") cmd.delete('Adjacent') except: import tkMessageBox tkMessageBox.showinfo('Alert', 'You must load a motif first') interior.mainloop() delres.bind('', resdel) #Mofit Finder--------------------------------- #------Goes through all motif functions and counts atoms for viable returns group = Pmw.Group(page, tag_text='Motif Search') group.grid(row=4, column=1, columnspan=1, padx=2, pady=2, sticky=W) interior = group.interior() def motifchecker(event): cmd.hide('everything', 'all') cmd.remove("(all) and hydro") list=[] self.exonucleaseiii2() x = cmd.count_atoms('Exonuclease3') if x == 42: list.append