Difference between revisions of "Rotamer Toggle"

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===DESCRIPTION===
 
===DESCRIPTION===
 
Backbone-Dependent Rotamer library (Dunbrack, Cohen ; see ref) is imported into pymol giving access to this information.  There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful.
 
Backbone-Dependent Rotamer library (Dunbrack, Cohen ; see ref) is imported into pymol giving access to this information.  There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful.
 +
*Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well
 
*colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common).
 
*colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common).
−
*Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well
 
 
*set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
 
*set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
−
*set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)  
+
*set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)
 +
*createRotamerPDBs - create pdb for each rotamer of given selection ; filter by rotamer-probability
 +
 
 +
===IMAGES===
 +
<gallery>
 +
Image:RotamerMenu.png|Rotamer Menu for a GLN residue
 +
Image:GLURotamerComparison5.png|Rotamer Comparison of crystal structure and most common for GLU; just as an example
 +
</gallery>
 +
 
 +
Print out while selecting most common rotamer from above-left image (GLN residue):
 +
  Given GLN:40 PHI,PSI (-171.626373291,-96.0500335693) : bin (-170,-100)
 +
  CHIs: [179.18069458007812, 72.539344787597656, -47.217315673828125]
 +
  Setting Chi1 to -176.9
 +
  Setting Chi2 to 177.4
 +
  Setting Chi3 to 0.7
 +
 
 +
===SETUP===
 +
run "rotamers.py" and use functions from commandline.
 +
 
 +
or
  
 
To setup a rotamer menu inside the residue menu (default windows pymol installation):
 
To setup a rotamer menu inside the residue menu (default windows pymol installation):
Line 12: Line 31:
 
This is only one possible way to do this, I am sure there are many others. I'm not going to post the bbdep, but there is a link in the References section to Dunbrack's download page (get the "sorted" lib)
 
This is only one possible way to do this, I am sure there are many others. I'm not going to post the bbdep, but there is a link in the References section to Dunbrack's download page (get the "sorted" lib)
  
−
Of course you can simply import rotamers.py and use the functions manually.
+
===NOTES / STATUS===
 +
*Tested on Pymolv0.97, Windows platform, Red Hat Linux 9.0 and Fedora Core 4. Will test v0.98 and MacOSX later on.
 +
*The way it's setup now, when you import rotamers , it will automatically read-in the rotamer database; this may not be what you want.
 +
*Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu
 +
 
 +
TASKS TODO:
 +
*Rotamer Movie, using mset, etc create movie to watch cycle through rotamers
 +
*Code could be organized a bit better; due to time constraints this is good for now..
  
−
This should not have any OS specific stuff in it yet, but has only been tested on Windows. I'll test it on linux in the next few days.
+
TASKS DONE:
 +
*Store crystal structure in rotamer menu, so you can go back to original orientation
  
 
===USAGE===
 
===USAGE===
Line 20: Line 47:
 
  set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle]
 
  set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle]
 
  set_phipsi selection phi_angle, psi_angle
 
  set_phipsi selection phi_angle, psi_angle
 +
createRotamerPBDs selection [,ncutoff] [,pcutoff] [,prefix]
  
 
===EXAMPLES===
 
===EXAMPLES===
Line 25: Line 53:
 
   set_rotamer resi 40, -60,-40  (only set chi1,chi2 angles)
 
   set_rotamer resi 40, -60,-40  (only set chi1,chi2 angles)
 
   set_phipsi resi 10-40, -60,-60 (create an alpha-helical-like section)
 
   set_phipsi resi 10-40, -60,-60 (create an alpha-helical-like section)
−
    
+
   createRotamerPDBs resi 10-12, ncutoff=3 (create 9 PDBs; each with one of the 3 most probable rotamers for resi 10,11,12)
 +
  createRotamerPDBs resi 14, pcutoff=0.4  (create a pdb file for each rotamer of residue 14 with probablity > 0.4)
 +
 
 
===REFERENCES===
 
===REFERENCES===
 
Dunbrack and Cohen. Protein Science 1997
 
Dunbrack and Cohen. Protein Science 1997
Line 31: Line 61:
 
[http://dunbrack.fccc.edu/bbdep/index.php Dunbrack Lab Page (Contains backbone-dependent library)]
 
[http://dunbrack.fccc.edu/bbdep/index.php Dunbrack Lab Page (Contains backbone-dependent library)]
  
−
===Scripts (Rotamers.py ; MyMenu.py)===
+
===SCRIPTS (Rotamers.py ; MyMenu.py)===
 
Rotamers.py  
 
Rotamers.py  
 
  <source lang="python">
 
  <source lang="python">
−
  ##################################################################
+
##################################################################
 
# File:          Rotamers.py
 
# File:          Rotamers.py
 
# Author:        Dan Kulp
 
# Author:        Dan Kulp
 
# Creation Date: 6/8/05
 
# Creation Date: 6/8/05
 +
# Contact:      dwkulp@mail.med.upenn.edu
 
#
 
#
 
# Notes:
 
# Notes:
Line 50: Line 81:
 
#          phi,psi bin for rotamer
 
#          phi,psi bin for rotamer
 
#    3. set_rotamer - set a side-chain  
 
#    3. set_rotamer - set a side-chain  
−
#          to a specific rotamer
+
#          to a specific rotamer
 
#
 
#
 
#    To setup a rotamer menu in the  
 
#    To setup a rotamer menu in the  
Line 62: Line 93:
 
#  Dunbrack and Cohen. Protein Science 1997
 
#  Dunbrack and Cohen. Protein Science 1997
 
####################################################################
 
####################################################################
−
 
+
 
import colorsys,sys
 
import colorsys,sys
−
import string
 
−
import re
 
 
import editing
 
import editing
 
import os
 
import os
 
import cmd
 
import cmd
 
import math
 
import math
−
 
+
 
# Path for library
 
# Path for library
 
ROTLIB=os.environ['PYMOL_PATH']+"/modules/pymol/bbdep02.May.sortlib"
 
ROTLIB=os.environ['PYMOL_PATH']+"/modules/pymol/bbdep02.May.sortlib"
−
 
+
 
# Place for library in memory..
 
# Place for library in memory..
 
rotdat = {}
 
rotdat = {}
−
 
+
−
def readRotLib():
+
def readRotLib():
 
     # Column indexes in rotamer library..
 
     # Column indexes in rotamer library..
 
     RES  = 0
 
     RES  = 0
Line 87: Line 116:
 
     CHI3 = 11
 
     CHI3 = 11
 
     CHI4 = 12
 
     CHI4 = 12
−
 
+
 
     if os.path.exists(ROTLIB):
 
     if os.path.exists(ROTLIB):
−
print "File exists: "+ROTLIB
+
                print "File exists: "+ROTLIB
−
input = open(ROTLIB, 'r')
+
                input = open(ROTLIB, 'r')
−
for line in input:
+
                for line in input:
−
 
+
−
      # Parse by whitespace (I believe format is white space and not fixed-width columns)
+
                    # Parse by whitespace (I believe format is white space and not fixed-width columns)
−
    dat = re.split("\s+",line)
+
                    dat = line.split()
−
 
+
−
    # Add to rotamer library in memory :  
+
                    # Add to rotamer library in memory :  
−
    #  key format      RES:PHI_BIN:PSI_BIN
+
                    #  key format      RES:PHI_BIN:PSI_BIN
−
    #  value format    PROB, CHI1, CHI2, CHI3, CHI4
+
                    #  value format    PROB, CHI1, CHI2, CHI3, CHI4
−
    try:
+
                    key=dat[RES]+":"+dat[PHI]+":"+dat[PSI]
−
        rotdat[dat[RES]+":"+dat[PHI]+":"+dat[PSI]].append([ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ])
+
                    if key in rotdat:
−
    except KeyError:
+
                        rotdat[key].append([ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ])
−
rotdat[dat[RES]+":"+dat[PHI]+":"+dat[PSI]] = [ [ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ] ]
+
                    else:
−
 
+
                        rotdat[key] = [ [ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ] ]
−
   
+
 +
 
     else:
 
     else:
−
print "Couldn't find Rotamer library"
+
        print "Couldn't find Rotamer library"
−
 
+
−
 
+
 
# Atoms for each side-chain angle for each residue
 
# Atoms for each side-chain angle for each residue
 
CHIS = {}
 
CHIS = {}
 
CHIS["ARG"] = [ ["N","CA","CB","CG" ],
 
CHIS["ARG"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD" ],
+
                ["CA","CB","CG","CD" ],
−
["CB","CG","CD","NE" ],
+
                ["CB","CG","CD","NE" ],
−
["CG","CD","NE","CZ" ]
+
                ["CG","CD","NE","CZ" ]
−
      ]
+
              ]
−
 
+
 
CHIS["ASN"] = [ ["N","CA","CB","CG" ],
 
CHIS["ASN"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","OD2" ]
+
                ["CA","CB","CG","OD2" ]
−
      ]
+
              ]
−
 
+
 
CHIS["ASP"] = [ ["N","CA","CB","CG" ],
 
CHIS["ASP"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","OD1" ]
+
                ["CA","CB","CG","OD1" ]
−
      ]
+
              ]
−
CHIS["CYS"] = [ ["N","CA","CB","CG" ]
+
CHIS["CYS"] = [ ["N","CA","CB","SG" ]
−
      ]
+
              ]
 +
 
CHIS["GLN"] = [ ["N","CA","CB","CG" ],
 
CHIS["GLN"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD" ],
+
                ["CA","CB","CG","CD" ],
−
["CB","CG","CD","OE1"]
+
                ["CB","CG","CD","OE1"]
−
      ]
+
              ]
−
 
+
 
CHIS["GLU"] = [ ["N","CA","CB","CG" ],
 
CHIS["GLU"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD" ],
+
                ["CA","CB","CG","CD" ],
−
["CB","CG","CD","OE1"]
+
                ["CB","CG","CD","OE1"]
−
      ]
+
              ]
−
 
+
 
CHIS["HIS"] = [ ["N","CA","CB","CG" ],
 
CHIS["HIS"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","ND1"]
+
                ["CA","CB","CG","ND1"]
−
      ]
+
              ]
−
 
+
 
CHIS["ILE"] = [ ["N","CA","CB","CG1" ],
 
CHIS["ILE"] = [ ["N","CA","CB","CG1" ],
−
["CA","CB","CG1","CD1" ]
+
                ["CA","CB","CG1","CD1" ]
−
      ]
+
              ]
−
 
+
 
CHIS["LEU"] = [ ["N","CA","CB","CG" ],
 
CHIS["LEU"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD1" ]
+
                ["CA","CB","CG","CD1" ]
−
      ]
+
              ]
−
 
+
 
CHIS["LYS"] = [ ["N","CA","CB","CG" ],
 
CHIS["LYS"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD" ],
+
                ["CA","CB","CG","CD" ],
−
["CB","CG","CD","CE"],
+
                ["CB","CG","CD","CE"],
−
["CG","CD","CE","NZ"]
+
                ["CG","CD","CE","NZ"]
−
      ]
+
              ]
−
 
+
 
CHIS["MET"] = [ ["N","CA","CB","CG" ],
 
CHIS["MET"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","SD" ],
+
                ["CA","CB","CG","SD" ],
−
["CB","CG","SD","CE"]
+
                ["CB","CG","SD","CE"]
−
      ]
+
              ]
−
 
+
 
CHIS["PHE"] = [ ["N","CA","CB","CG" ],
 
CHIS["PHE"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD1" ]
+
                ["CA","CB","CG","CD1" ]
−
      ]
+
              ]
−
 
+
 
CHIS["PRO"] = [ ["N","CA","CB","CG" ],
 
CHIS["PRO"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD" ]
+
                ["CA","CB","CG","CD" ]
−
      ]
+
              ]
−
 
+
 
CHIS["SER"] = [ ["N","CA","CB","OG" ]
 
CHIS["SER"] = [ ["N","CA","CB","OG" ]
−
      ]
+
              ]
−
 
+
 
CHIS["THR"] = [ ["N","CA","CB","OG1" ]
 
CHIS["THR"] = [ ["N","CA","CB","OG1" ]
−
      ]
+
              ]
 +
 +
CHIS["TRP"] = [ ["N","CA","CB","CG" ],
 +
                ["CA","CB","CG","CD1"]
 +
              ]
 +
 
CHIS["TYR"] = [ ["N","CA","CB","CG" ],
 
CHIS["TYR"] = [ ["N","CA","CB","CG" ],
−
["CA","CB","CG","CD1" ]
+
                ["CA","CB","CG","CD1" ]
−
      ]
+
              ]
−
 
+
 
CHIS["VAL"] = [ ["N","CA","CB","CG1" ]
 
CHIS["VAL"] = [ ["N","CA","CB","CG1" ]
−
      ]
+
              ]
−
 
+
 
# Color Rotamer by side-chain angle position
 
# Color Rotamer by side-chain angle position
 
#  'bin' side-chain angles into closest
 
#  'bin' side-chain angles into closest
 
def colorRotamers(sel):
 
def colorRotamers(sel):
 
     doRotamers(sel)
 
     doRotamers(sel)
−
 
+
 
# Utility function, to set phi,psi angles for a given selection
 
# Utility function, to set phi,psi angles for a given selection
 
# Note: Cartoon, Ribbon functionality will not display correctly after this
 
# Note: Cartoon, Ribbon functionality will not display correctly after this
 
def set_phipsi(sel, phi,psi):
 
def set_phipsi(sel, phi,psi):
 
     doRotamers(sel,angles=[phi,psi],type="set")
 
     doRotamers(sel,angles=[phi,psi],type="set")
−
 
+
 
# Set a rotamer, based on a selection, a restype and chi angles
 
# Set a rotamer, based on a selection, a restype and chi angles
 
def set_rotamer(sel, chi1, chi2=0,chi3=0,chi4=0):
 
def set_rotamer(sel, chi1, chi2=0,chi3=0,chi4=0):
 
     at = cmd.get_model("byres ("+sel+")").atom[0]
 
     at = cmd.get_model("byres ("+sel+")").atom[0]
−
 
+
 
     list = [chi1,chi2,chi3,chi4]
 
     list = [chi1,chi2,chi3,chi4]
−
     for i in range(0,len(CHIS[at.resn])):
+
     for i in range(len(CHIS[at.resn])):
−
print "Setting Chi"+str(i+1)+" to "+str(list[i])
+
        print "Setting Chi"+str(i+1)+" to "+str(list[i])
−
         editing.set_dihedral(sel + ' and name '+CHIS[at.resn][i][0],    
+
         editing.set_dihedral(sel + ' and name '+CHIS[at.resn][i][0],
−
            sel + ' and name '+CHIS[at.resn][i][1],    
+
                            sel + ' and name '+CHIS[at.resn][i][1],
−
            sel + ' and name '+CHIS[at.resn][i][2],    
+
                            sel + ' and name '+CHIS[at.resn][i][2],
−
            sel + ' and name '+CHIS[at.resn][i][3], list[i])    
+
                            sel + ' and name '+CHIS[at.resn][i][3], str(list[i]))
−
 
+
 
     # Remove some objects that got created
 
     # Remove some objects that got created
 
     cmd.delete("pk1")
 
     cmd.delete("pk1")
 
     cmd.delete("pk2")
 
     cmd.delete("pk2")
 
     cmd.delete("pkmol")
 
     cmd.delete("pkmol")
−
 
+
 
# Get Phi,Psi bins for given selection
 
# Get Phi,Psi bins for given selection
 
# WARNING:  assume selection is single residue (will only return first residue bins)
 
# WARNING:  assume selection is single residue (will only return first residue bins)
 
def getBins(sel):
 
def getBins(sel):
 
     return doRotamers(sel, type="bins")
 
     return doRotamers(sel, type="bins")
−
 
+
−
# Specific comparison operator for rotamer prob data
 
−
def mycmp(first, second):
 
−
return cmp( first[1], second[1])
 
−
 
 
 
# Color Ramp...
 
# Color Ramp...
 
def rot_color(vals):  
 
def rot_color(vals):  
−
nbins = 10
+
        nbins = 10
−
vals.sort(mycmp)
+
        vals.sort(key=lambda x:x[1])
−
print "End sort: "+str(len(vals))+" : "+str(nbins)
+
#      print "End sort: "+str(len(vals))+" : "+str(nbins)
−
 
+
−
 
+
−
# Coloring scheme...
+
        # Coloring scheme...
−
i = 0
+
        j = 0
−
j = 0
+
        rgb = [0.0,0.0,0.0]
−
rgb = [0.0,0.0,0.0]
+
        sel_str = ""
−
sel_str = ""
+
        for i in range(len(vals)):
−
while i < len(vals):
+
                if int(len(vals)/nbins) == 0 or i % int(len(vals)/nbins) == 0:
−
if int(len(vals)/nbins) == 0 or i % int(len(vals)/nbins) == 0:
+
                      hsv = (colorsys.TWO_THIRD - colorsys.TWO_THIRD * float(j) / (nbins-1), 1.0, 1.0)
−
      hsv = (colorsys.TWO_THIRD - colorsys.TWO_THIRD * float(j) / (nbins-1), 1.0, 1.0)
+
−
 
+
                      #convert to rgb and append to color list
−
      #convert to rgb and append to color list
+
                      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
−
      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
+
                      if j < nbins-1:
−
      if j < nbins-1:
+
                              j += 1
−
              j += 1
+
−
 
+
                cmd.set_color("RotProbColor"+str(i), rgb)
−
cmd.set_color("RotProbColor"+str(i), rgb)
+
                cmd.color("RotProbColor"+str(i), str(vals[i][0]))
−
cmd.color("RotProbColor"+str(i), str(vals[i][0]))
+
−
i += 1
+
−
 
+
# Main function
−
 
+
def doRotamers(sel,angles=[], type="color"):
−
# Main function                          
+
−
def doRotamers(sel,angles=[], type="color"):                          
+
        # Read in Rotamer library if not already done
−
 
+
        if len(rotdat) == 0:
−
# Read in Rotamer library if not already done
+
                readRotLib()
−
if len(rotdat) == 0:
+
−
readRotLib()
+
        # Set up some variables..
−
 
+
        residues = ['dummy']  # Keep track of residues already done
−
# Set up some variables..
+
        probs = []            # probability of each residue conformation
−
residues = ['dummy']  # Keep track of residues already done
+
        phi = 0              # phi,psi angles of current residue
−
probs = []            # probability of each residue conformation
+
        psi = 0
−
phi = 0              # phi,psi angles of current residue
+
−
psi = 0
+
        # Get atoms from selection
−
 
+
        atoms = cmd.get_model("byres ("+sel+")")
−
# Get atoms from selection
+
−
atoms = cmd.get_model("byres ("+sel+")")
+
         # Loop through atoms in selection
−
 
+
        for at in atoms.atom:
−
         # Loop through atoms in selection
+
            try:
−
for at in atoms.atom:
+
              # Don't process Glycines or Alanines
−
    try:
+
              if not (at.resn == 'GLY' or at.resn == 'ALA'):
−
      # Don't process Glycines or Alanines
+
                if at.chain+":"+at.resn+":"+at.resi not in residues:
−
      if not (at.resn == 'GLY' or at.resn == 'ALA'):
+
                    residues.append(at.chain+":"+at.resn+":"+at.resi)
−
        if not at.chain+":"+at.resn+":"+at.resi in residues:
+
−
            residues.append(at.chain+":"+at.resn+":"+at.resi)
+
                    # Check for a null chain id (some PDBs contain this)  
−
 
+
                    unit_select = ""
−
    # Check for a null chain id (some PDBs contain this)  
+
                    if at.chain != "":
−
    unit_select = ""
+
                        unit_select = "chain "+str(at.chain)+" and "
−
    if not at.chain == "":
+
−
unit_select = "chain "+str(at.chain)+" and "
+
                    # Define selections for residue i-1, i and i+1
−
 
+
                    residue_def = unit_select+'resi '+str(at.resi)
−
    # Define selections for residue i-1, i and i+1  
+
                    residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
−
    residue_def = unit_select+'resi '+str(at.resi)
+
                    residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
−
      residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
+
−
    residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
+
                    # Compute phi/psi angle
−
 
+
−
            # Compute phi/psi angle
+
                    phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C')
−
    phi = cmd.get_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C')
+
                    psi = cmd.get_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N')
−
    psi = cmd.get_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB')
+
                    if type == "set":
−
    if type == "set":
+
                            print "Changing "+at.resn+str(at.resi)+" from "+str(phi)+","+str(psi)+" to "+str(angles[0])+","+str(angles[1])
−
    print "Changing "+at.resn+str(at.resi)+" from "+str(phi)+","+str(psi)+" to "+str(angles[0])+","+str(angles[1])
+
                            cmd.set_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',angles[0])
−
    cmd.set_dihedral(residue_def+' and name CB',residue_def+' and name CA',residue_def+' and name N',residue_def_prev+' and name C',angles[0])
+
                            cmd.set_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N', angles[1])
−
    cmd.set_dihedral(residue_def+' and name O',residue_def+' and name C',residue_def+' and name CA',residue_def+' and name CB', angles[1])
+
                            continue
−
    continue
+
−
+
                    # Find correct 10x10 degree bin                                    
−
    # Find correct 10x10 degree bin        
+
                    phi_digit = abs(int(phi)) - abs(int(phi/10)*10)
−
    phi_digit = abs(int(phi)) - abs(int(phi/10)*10)
+
                    psi_digit = abs(int(psi)) - abs(int(psi/10)*10)
−
    psi_digit = abs(int(psi)) - abs(int(psi/10)*10)
+
−
   
+
                    # Remember sign of phi,psi angles
−
    # Remember sign of phi,psi angles
+
                    phi_sign = 1
−
        phi_sign = 1
+
                    if phi < 0:    phi_sign = -1
−
    if phi < 0:    phi_sign = -1
+
−
 
+
                    psi_sign = 1
−
    psi_sign = 1
+
                    if psi < 0:    psi_sign = -1
−
    if psi < 0:    psi_sign = -1
+
−
 
+
                    # Compute phi,psi bins
−
    # Compute phi,psi bins
+
                    phi_bin = int(math.floor(abs(phi/10))*10*phi_sign)
−
      phi_bin = int(math.floor(abs(phi/10))*10*phi_sign)
+
                    if phi_digit >= 5:    phi_bin = int(math.ceil(abs(phi/10))*10*phi_sign)
−
    if phi_digit >= 5:    phi_bin = int(math.ceil(abs(phi/10))*10*phi_sign)
+
−
 
+
                    psi_bin = int(math.floor(abs(psi/10))*10*psi_sign)
−
    psi_bin = int(math.floor(abs(psi/10))*10*psi_sign)
+
                    if psi_digit >= 5:    psi_bin = int(math.ceil(abs(psi/10))*10*psi_sign)
−
    if psi_digit >= 5:    psi_bin = int(math.ceil(abs(psi/10))*10*psi_sign)
+
−
 
+
                    print "Given "+at.resn+":"+at.resi+" PHI,PSI ("+str(phi)+","+str(psi)+") : bin ("+str(phi_bin)+","+str(psi_bin)+")"
−
            print "Given "+at.resn+":"+at.resi+" PHI,PSI ("+str(phi)+","+str(psi)+") : bin ("+str(phi_bin)+","+str(psi_bin)+")"
+
−
 
+
−
+
                    # Get current chi angle measurements
−
    # Get current chi angle measurements
+
                    chi = []
−
    chi = []
+
                    for i in range(len(CHIS[at.resn])):
−
    for i in range(0,len(CHIS[at.resn])):
+
                      chi.append(cmd.get_dihedral(residue_def + ' and name '+CHIS[at.resn][i][0],
−
      chi.append(cmd.get_dihedral(residue_def + ' and name '+CHIS[at.resn][i][0],    
+
                                                    residue_def + ' and name '+CHIS[at.resn][i][1],
−
              residue_def + ' and name '+CHIS[at.resn][i][1],    
+
                                                    residue_def + ' and name '+CHIS[at.resn][i][2],
−
            residue_def + ' and name '+CHIS[at.resn][i][2],    
+
                                                    residue_def + ' and name '+CHIS[at.resn][i][3]))
−
            residue_def + ' and name '+CHIS[at.resn][i][3]))    
+
                    print "CHIs: "+str(chi)
−
    print "CHIs: "+str(chi)
+
                    if type == 'bins':
−
    if type == 'bins':
+
                        return [at.resn, phi_bin,psi_bin]
−
        return [at.resn, phi_bin,psi_bin]
+
−
 
+
                    # Compute probabilities for given chi angles
−
    # Compute probabilities for given chi angles
 
 
                     prob = 0
 
                     prob = 0
−
    prob_box = 22    
+
                    prob_box = 22                  
−
    for item in range(0,len(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)])):
+
                    for item in range(len(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)])):
−
print "Rotamer from db: "+str(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item])
+
                        print "Rotamer from db: "+str(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item])
−
if chi[0]:
+
                        if chi[0]:
−
    if chi[0] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) - (prob_box/2) and \
+
                            if chi[0] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) - (prob_box/2) and \
−
chi[0] <= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) + (prob_box/2):
+
                                chi[0] <= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) + (prob_box/2):
−
if len(chi) == 1:
+
                                if len(chi) == 1:
−
prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
+
                                        prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
−
break
+
                                        break
−
if chi[1] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) - (prob_box/2) and \
+
                                if chi[1] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) - (prob_box/2) and \
−
float(chi[1] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) + (prob_box/2):
+
                                float(chi[1] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) + (prob_box/2):
−
if len(chi) == 2:
+
                                        if len(chi) == 2:
−
    prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
+
                                            prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
−
    break
+
                                            break
−
if chi[2] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) - (prob_box/2) and \
+
                                        if chi[2] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) - (prob_box/2) and \
−
  float(chi[2] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) + (prob_box/2):
+
                                          float(chi[2] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) + (prob_box/2):
−
        if len(chi) == 3:
+
                                            if len(chi) == 3:
−
        prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
+
                                                prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
−
        break
+
                                                break
−
    if chi[3] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) - (prob_box/2) and \
+
                                            if chi[3] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) - (prob_box/2) and \
−
      float(chi[3] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) + (prob_box/2):
+
                                              float(chi[3] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) + (prob_box/2):
−
        prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
+
                                                prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
−
        break
+
                                                break
−
 
+
−
+
−
    print "PROB OF ROTAMER: "+str(prob)
+
                    print "PROB OF ROTAMER: "+str(prob)
−
    print "---------------------------"
+
                    print "---------------------------"
−
    probs.append([residue_def, prob])
+
                    probs.append([residue_def, prob])
−
 
+
−
    except:
+
            except:
−
# probs.append([residue_def, -1])
+
#               probs.append([residue_def, -1])
−
print "Exception found"
+
                print "Exception found"
−
continue
+
                continue
−
 
+
−
# Color according to rotamer probability
+
        # Color according to rotamer probability
−
rot_color(probs)    
+
        rot_color(probs)
−
 
+
−
+
−
 
+
−
 
+
−
 
+
#  Create PDB files containing most probable rotamers
−
 
+
def createRotamerPDBs(sel,ncutoff=10,pcutoff=0,prefix="ROTAMER"):
−
readRotLib()
+
−
 
+
        # Get atoms from selection
 +
        atoms = cmd.get_model("byres ("+sel+")")
 +
 +
        # Set up some variables..
 +
        residues = ['dummy']  # Keep track of residues already done
 +
 +
        # Loop through atoms in selection
 +
        for at in atoms.atom:
 +
                if at.resn in ('GLY','ALA') or "%s:%s:%s" % (at.chain,at.resn,at.resi) in residues:
 +
                        continue
 +
 +
                # Add to residue list (keep track of which ones we've done)
 +
                residues.append("%s:%s:%s" % (at.chain,at.resn,at.resi))
 +
 +
                # Check for a null chain id (some PDBs contain this)
 +
                unit_select = ""
 +
                if not at.chain == "":
 +
                    unit_select = "chain "+str(at.chain)+" and "
 +
 +
                # Define selections for residue
 +
                residue_def = unit_select+'resi '+str(at.resi)
 +
 +
                # Get bin (phi,psi) definitions for this residue
 +
                bin = doRotamers(residue_def, type='bins')
 +
 +
                # Store crystal angle
 +
                crystal_angles = [0.0,0.0,0.0,0.0]
 +
                for angle in range(3):
 +
                        try:
 +
                                crystal_angles[angle] = bin[3][angle]
 +
                        except IndexError:
 +
                                break
 +
 +
                # Retreive list of rotamers for this phi,psi bin + residue type
 +
                match_rotamers = rotdat["%s:%s:%s" % (bin[0],str(bin[1]),str(bin[2]))]
 +
 +
                count = 0
 +
                for item in range(len(match_rotamers)):
 +
 +
                        # Store probablity
 +
                        prob = match_rotamers[item][0]
 +
 +
                        # Check cutoffs
 +
                        if float(prob) <= float(pcutoff):
 +
                                continue
 +
 +
                        if float(count) >= float(ncutoff):
 +
                                break
 +
 +
                        # Increment count
 +
                        count += 1
 +
 +
                        # Output to screen ...
 +
                        print "Residue %s%s, rotamer %i, prob %s" % (str(at.resn),str(at.resi),int(item),str(prob))
 +
 +
                        # Set to new rotamer
 +
                        set_rotamer(residue_def,match_rotamers[item][1],match_rotamers[item][2],match_rotamers[item][3],match_rotamers[item][4])                                                                                               
 +
 +
                        # Store in PDB file
 +
                        cmd.save("%s_%s%s_%i_%s.pdb" % (prefix,str(at.resn),str(at.resi),int(item),str(prob)))
 +
 +
                        # Reset crystal angle
 +
                        set_rotamer(residue_def,crystal_angles[0],crystal_angles[1],crystal_angles[2],crystal_angles[3])
 +
 +
# Uncommenting this is nice because it loads rotamer library upon startup
 +
#  however, it slows the PyMOL loading process a lot
 +
#  instead I've put this call into the menuing code..
 +
# readRotLib()
 +
 
cmd.extend('set_phipsi',set_phipsi)
 
cmd.extend('set_phipsi',set_phipsi)
 
cmd.extend('set_rotamer',set_rotamer)
 
cmd.extend('set_rotamer',set_rotamer)
 
cmd.extend('colorRotamers',colorRotamers)
 
cmd.extend('colorRotamers',colorRotamers)
 +
cmd.extend('createRotamerPDBs',createRotamerPDBs)
 +
</source>
  
−
  </source>
+
MyMenu.py
 +
  Since menu.py is copyrighted I can't post my edited version, but you can create it very simply by adding these two peices of code
  
−
MyMenu.py
+
1. In the "pick_option(title,s,object=0)" function of menu.py add the following code after the first "result =" statement
 
<source lang="python">
 
<source lang="python">
−
#A* -------------------------------------------------------------------
 
−
#B* This file contains source code for the PyMOL computer program
 
−
#C* copyright 1998-2000 by Warren Lyford Delano of DeLano Scientific.
 
−
#D* -------------------------------------------------------------------
 
−
#E* It is unlawful to modify or remove this copyright notice.
 
−
#F* -------------------------------------------------------------------
 
−
#G* Please see the accompanying LICENSE file for further information.
 
−
#H* -------------------------------------------------------------------
 
−
#I* Additional authors of this source file include:
 
−
#-* Dan Kulp (dwkulp@mail.med.upenn.edu) ; rotamer menu
 
−
#-*
 
−
#-*
 
−
#Z* -------------------------------------------------------------------
 
−
 
−
# pmm.py
 
−
# This section contains the menu contents and the associated commands
 
−
#
 
−
 
−
import cmd
 
−
import os
 
−
 
−
def mol_show(s):
 
−
  return [[ 2, 'Show:'      , ''                              ],
 
−
          [ 1, 'lines'      , 'cmd.show("lines"    ,"'+s+'")' ],
 
−
          [ 1, 'nonbonded'  , 'cmd.show("nonbonded" ,"'+s+'")' ],
 
−
          [ 1, 'sticks'    , 'cmd.show("sticks"    ,"'+s+'")' ],
 
−
          [ 1, 'ribbon'    , 'cmd.show("ribbon"    ,"'+s+'")' ],
 
−
          [ 1, 'cartoon'    , 'cmd.show("cartoon"  ,"'+s+'")' ],
 
−
          [ 0, ''          , ''                              ],
 
−
          [ 1, 'labels'    , 'cmd.show("labels"    ,"'+s+'")' ],
 
−
          [ 1, 'cell'      , 'cmd.show("cell"      ,"'+s+'")' ],
 
−
          [ 0, ''          , ''                              ],
 
−
          [ 1, 'dots'      , 'cmd.show("dots"      ,"'+s+'")' ],
 
−
          [ 1, 'spheres'    , 'cmd.show("spheres"  ,"'+s+'")' ],
 
−
          [ 1, 'nb_spheres' , 'cmd.show("nb_spheres","'+s+'")' ],
 
−
          [ 0, ''          , ''                              ],
 
−
          [ 1, 'mesh'      , 'cmd.show("mesh"      ,"'+s+'")' ],
 
−
          [ 1, 'surface'    , 'cmd.show("surface"  ,"'+s+'")' ],
 
−
          [ 0, ''          , ''                              ],         
 
−
          [ 1, 'main chain' , 'cmd.show("lines","((byres ('+s+'))&n;ca,c,n,o,h)")' ],
 
−
          [ 1, 'side chain' , 'cmd.show("lines","((byres ('+s+'))&(!n;c,n,o,h))")' ],
 
−
          ]
 
−
 
−
def mol_hide(s):
 
−
  return [[ 2, 'Hide:'    , ''                                ],
 
−
          [ 1, 'everything', 'cmd.hide("everything","'+s+'")'  ],
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'lines'    , 'cmd.hide("lines"    ,"'+s+'")'  ],
 
−
          [ 1, 'nonbonded' , 'cmd.hide("nonbonded" ,"'+s+'")'  ],         
 
−
          [ 1, 'sticks'    , 'cmd.hide("sticks"    ,"'+s+'")'  ],
 
−
          [ 1, 'ribbon'    , 'cmd.hide("ribbon"    ,"'+s+'")'  ],
 
−
          [ 1, 'cartoon'  , 'cmd.hide("cartoon"  ,"'+s+'")' ],         
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'labels'    , 'cmd.hide("labels"    ,"'+s+'")'  ],
 
−
          [ 1, 'cell'      , 'cmd.hide("cell"      ,"'+s+'")' ],
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'dots'      , 'cmd.hide("dots"      ,"'+s+'")'  ],
 
−
          [ 1, 'spheres'  , 'cmd.hide("spheres"  ,"'+s+'")'  ],
 
−
          [ 1, 'nb_spheres', 'cmd.hide("nb_spheres","'+s+'")'  ],         
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'mesh'      , 'cmd.hide("mesh"      ,"'+s+'")'  ],
 
−
          [ 1, 'surface'  , 'cmd.hide("surface"  ,"'+s+'")'  ],
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'main chain', 'cmd.hide("((byres ('+s+'))&n;c,n,o,h)")' ],
 
−
          [ 1, 'side chain', 'cmd.hide("((byres ('+s+'))&!n;ca,c,n,o,h)")' ],
 
−
          [ 1, 'waters'    , 'cmd.hide("(resn HOH+WAT and ('+s+'))")'    ],                     
 
−
          [ 0, ''          , ''                                ],
 
−
          [ 1, 'hydrogens' , 'cmd.hide("('+s+' and hydro)")'  ],
 
−
          [ 0, ''          , ''                                ],         
 
−
          [ 1, 'unselected', 'cmd.hide("(not '+s+')")'        ],
 
−
          ]
 
−
 
−
def dist_show(s):
 
−
  return [[ 2, 'Show:'    , ''                              ],
 
−
          [ 1, 'dashes'    , 'cmd.show("dashes"    ,"'+s+'")' ],
 
−
          [ 1, 'labels'    , 'cmd.show("labels"    ,"'+s+'")' ]
 
−
          ] 
 
−
 
−
def dist_hide(s):
 
−
  return [[ 2, 'Hide:'    , ''                                ],
 
−
          [ 1, 'dashes'    , 'cmd.hide("dashes"    ,"'+s+'")'  ],
 
−
          [ 1, 'labels'    , 'cmd.hide("labels"    ,"'+s+'")'  ]
 
−
          ]
 
−
 
−
def cgo_show(s):
 
−
  return [[ 2, 'Show:'    , ''                              ],
 
−
          [ 1, 'cgo'    , 'cmd.show("cgo"    ,"'+s+'")' ],
 
−
          ] 
 
−
 
−
def cgo_hide(s):
 
−
  return [[ 2, 'Hide:'    , ''                                ],
 
−
          [ 1, 'cgo'    , 'cmd.hide("cgo"    ,"'+s+'")'  ],
 
−
          ]
 
−
 
−
def simple_show(s):
 
−
  return [[ 2, 'Show:'      , ''                            ],
 
−
          [ 1, 'everything'  , 'cmd.show("everything","'+s+'")'          ]]
 
−
 
−
def simple_hide(s):
 
−
  return [[ 2, 'Hide:'    ,''                                ],
 
−
          [ 1, 'everything'    ,'cmd.hide("everything","'+s+'")'        ]]
 
−
 
−
def mesh_show(s):
 
−
  return [[ 2, 'Show:'      , ''                            ],
 
−
          [ 1, 'mesh'        , 'cmd.show("mesh","'+s+'")'    ],         
 
−
          [ 1, 'cell'        , 'cmd.show("cell","'+s+'")'    ],
 
−
          [ 1, 'everything'  , 'cmd.enable("'+s+'")'          ]]
 
−
 
−
def mesh_hide(s):
 
−
  return [[ 2, 'Hide:'      , ''                            ],
 
−
          [ 1, 'mesh'        , 'cmd.hide("mesh","'+s+'")'    ],                     
 
−
          [ 1, 'cell'        , 'cmd.hide("cell","'+s+'")'      ],         
 
−
          [ 1, 'everything'  , 'cmd.disable("'+s+'")'          ]]
 
−
 
−
def by_elem(s):
 
−
  return [
 
−
      [ 2, 'By Element:'    ,''                              ],
 
−
      [ 1, '\\292C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbag("'+s+'")'],
 
−
  [ 1, '\\099C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbac("'+s+'")'],
 
−
  [ 1, '\\909C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbam("'+s+'")'],         
 
−
  [ 1, '\\990C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbay("'+s+'")'],
 
−
  [ 1, '\\955C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbas("'+s+'")'],
 
−
  [ 1, '\\777C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbaw("'+s+'")'],
 
−
  [ 1, '\\559C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbab("'+s+'")'],
 
−
  [ 1, '\\972C\\777H\\229N\\922O\\950S\\905*'  , 'util.cbao("'+s+'")'],
 
−
  [ 1, ' \\777H\\229N\\922O\\950S\\905*'  , 'util.cnc("'+s+'")']]                   
 
−
 
−
def by_ss(s):
 
−
  return [
 
−
            [ 2, 'By Secondary Structure:'    ,''                              ],
 
−
  [ 1, '\\900Helix \\990Sheet \\090Loop'  , 'util.cbss("'+s+'","red","yellow","green")'],
 
−
  [ 1, '\\099Helix \\909Sheet \\955Loop'  , 'util.cbss("'+s+'","cyan","magenta","salmon")'],
 
−
          ]
 
−
 
−
def spectrum(s):
 
−
  return [
 
−
            [ 2, 'Spectrum:'    ,''                              ],
 
−
          [ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w\\888(e. c)',
 
−
            'cmd.spectrum("count",selection="('+s+')&e. c")'],         
 
−
          [ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w\\888(*/ca)',
 
−
            'cmd.spectrum("count",selection="('+s+')&*/ca")'],
 
−
          [ 1, '\\900r\\950a\\990i\\090n\\099b\\059o\\009w',
 
−
            'cmd.spectrum("count",selection="'+s+'",byres=1)'],
 
−
          [ 0, ''                                , ''                ],
 
−
          [ 1, 'b-factors'  , 'cmd.spectrum("b",selection=("'+s+'"))'        ],         
 
−
          ]
 
−
 
−
def by_chain(s):
 
−
  return [
 
−
      [ 2, 'By Chain:'    ,''                              ],
 
−
          [ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n\\888(e. c)',
 
−
            'util.color_chains("('+s+' and elem c)")'],
 
−
          [ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n\\888(*/ca)',
 
−
            'util.color_chains("('+s+' and name ca)")'],
 
−
          [ 1, '\\900b\\950y \\090c\\099h\\059a\\009i\\705n',
 
−
            'util.color_chains("('+s+')")'],
 
−
                [ 0, ''                                , ''                ],
 
−
          [ 1, '\\900c\\950h\\990a\\090i\\099n\\059b\\009o\\705w\\888s',
 
−
            'util.chainbow("('+s+')")'],                               
 
−
      ]
 
−
def mol_color(s):
 
−
  return [[ 2, 'Color:'    ,''                              ],
 
−
          [ 1, 'by chain' , by_chain(s) ],
 
−
          [ 1, 'by element'  , by_elem(s) ],
 
−
          [ 1, 'by ss  '  , by_ss(s) ],
 
−
          [ 1, '\\900s\\950p\\990e\\090c\\099t\\059r\\009u\\555m', spectrum(s) ],
 
−
          [ 0, ''                                , ''                ],         
 
−
          [ 1, '\\900red'        , 'cmd.color("red","'+s+'")'    ],
 
−
          [ 1, '\\090green'      , 'cmd.color("green","'+s+'")'  ],
 
−
          [ 1, '\\009blue'        , 'cmd.color("blue","'+s+'")'    ],
 
−
          [ 1, '\\990yellow'      , 'cmd.color("yellow","'+s+'")'  ],
 
−
          [ 1, '\\909magenta'    , 'cmd.color("magenta","'+s+'")' ],
 
−
          [ 1, '\\099cyan'        , 'cmd.color("cyan","'+s+'")'    ],         
 
−
          [ 1, '\\955salmon'      , 'cmd.color("salmon","'+s+'")'  ],
 
−
          [ 1, '\\595lime'        , 'cmd.color("lime","'+s+'")'    ],
 
−
          [ 1, '\\967pink'  ,'cmd.color("pink","'+s+'")'  ],
 
−
          [ 1, '\\559slate'      , 'cmd.color("slate","'+s+'")'  ],
 
−
          [ 1, '\\949violet'      , 'cmd.color("violet","'+s+'")'  ],
 
−
          [ 1, '\\950orange'      , 'cmd.color("orange","'+s+'")'  ],
 
−
          [ 1, '\\059marine'      , 'cmd.color("marine","'+s+'")'  ],
 
−
          [ 1, '\\905hotpink' ,'cmd.color("hotpink","'+s+'")'  ],
 
−
#          [ 1, '\\551olive'      , 'cmd.color("olive","'+s+'")'  ],
 
−
#          [ 1, '\\626purple'      , 'cmd.color("purple","'+s+'")'  ],
 
−
#          [ 1, '\\266teal'        , 'cmd.color("teal","'+s+'")'    ],
 
−
#          [ 1, '\\151forest'      , 'cmd.color("forest","'+s+'")'  ],
 
−
#          [ 1, '\\611firebrick'  , 'cmd.color("firebrick","'+s+'")'  ],
 
−
#          [ 1, '\\631chocolate'  , 'cmd.color("chocolate","'+s+'")'  ],         
 
−
          [ 1, '\\999white'      , 'cmd.color("white","'+s+'")'  ],
 
−
          [ 1, '\\987wheat'      , 'cmd.color("wheat","'+s+'")'  ],
 
−
          [ 1, '\\555grey'        , 'cmd.color("grey","'+s+'")'    ],
 
−
          [ 1, '\\222black'    ,'cmd.color("grey","'+s+'")'  ]
 
−
          ]
 
−
 
−
def general_color(s):
 
−
  return [[ 2, 'Color:'    ,''                        ],
 
−
          [ 1, '\\900red'        ,'cmd.color("red","'+s+'")'  ],
 
−
          [ 1, '\\090green'      ,'cmd.color("green","'+s+'")'  ],
 
−
          [ 1, '\\009blue'        ,'cmd.color("blue","'+s+'")'  ],
 
−
          [ 1, '\\990yellow'      ,'cmd.color("yellow","'+s+'")'  ],
 
−
          [ 1, '\\909magenta' ,'cmd.color("magenta","'+s+'")'  ],
 
−
          [ 1, '\\099cyan'  ,'cmd.color("cyan","'+s+'")'  ],         
 
−
          [ 1, '\\955salmon'      ,'cmd.color("salmon","'+s+'")'  ],
 
−
          [ 1, '\\595lime' ,'cmd.color("lime","'+s+'")'  ],
 
−
          [ 1, '\\967pink'  ,'cmd.color("pink","'+s+'")'  ],
 
−
          [ 1, '\\559slate'  ,'cmd.color("slate","'+s+'")'  ],
 
−
          [ 1, '\\949violet'  ,'cmd.color("violet","'+s+'")'  ],
 
−
          [ 1, '\\950orange'      ,'cmd.color("orange","'+s+'")'  ],
 
−
          [ 1, '\\059marine'      ,'cmd.color("marine","'+s+'")'  ],
 
−
          [ 1, '\\905hotpink' ,'cmd.color("hotpink","'+s+'")'  ],
 
−
#          [ 1, '\\551olive'  ,'cmd.color("olive","'+s+'")'  ],
 
−
#          [ 1, '\\626purple'  ,'cmd.color("purple","'+s+'")'  ],
 
−
#          [ 1, '\\266teal'  ,'cmd.color("teal","'+s+'")'  ],
 
−
#          [ 1, '\\151forest'  ,'cmd.color("forest","'+s+'")'  ],
 
−
#          [ 1, '\\611firebrick'  , 'cmd.color("firebrick","'+s+'")'  ],
 
−
#          [ 1, '\\631chocolate'  , 'cmd.color("chocolate","'+s+'")'  ],
 
−
          [ 1, '\\116density'    ,'cmd.color("density","'+s+'")'  ],
 
−
          [ 1, '\\999white'      ,'cmd.color("white","'+s+'")'  ],
 
−
          [ 1, '\\987wheat'      , 'cmd.color("wheat","'+s+'")'  ],
 
−
          [ 1, '\\555grey'    ,'cmd.color("grey","'+s+'")'  ],
 
−
          [ 1, '\\222black'    ,'cmd.color("grey","'+s+'")'  ]
 
−
          ]
 
−
 
−
def preset_ligand_sites(s):
 
−
  return [[ 2, 'Ligand Sites:', ''],
 
−
          [ 1, 'solid'  , 'preset.ligand_sites("'+s+'")'          ],
 
−
          [ 1, 'solid (better)'  , 'preset.ligand_sites_hq("'+s+'")'          ],
 
−
          [ 0, '', ''],
 
−
          [ 1, 'transparent'  , 'preset.ligand_sites_trans("'+s+'")'          ],
 
−
          [ 1, 'transparent (better)'  , 'preset.ligand_sites_trans_hq("'+s+'")'          ],
 
−
          [ 0, '', ''],
 
−
          [ 1, 'dot surface'  , 'preset.ligand_sites_dots("'+s+'")'          ],
 
−
          [ 0, '', ''],
 
−
          [ 1, 'mesh surface'  , 'preset.ligand_sites_mesh("'+s+'")'          ]]
 
−
 
−
def presets(s):
 
−
  return [[ 2, 'Preset:'      ,''                        ],   
 
−
          [ 1, 'simple'  ,'preset.simple("'+s+'")'          ],
 
−
          [ 1, 'simple (no solvent)'  ,'preset.simple_no_solv("'+s+'")'          ],         
 
−
          [ 1, 'technical'  , 'preset.technical("'+s+'")'          ],
 
−
          [ 1, 'ligands'  , 'preset.ligands("'+s+'")'          ],
 
−
          [ 1, 'ligand_sites'  , preset_ligand_sites(s)        ],
 
−
          [ 1, 'pretty ', 'preset.pretty("'+s+'")'          ],
 
−
          [ 1, 'pretty (with solvent)'    , 'preset.pretty_solv("'+s+'")'          ],
 
−
          [ 1, 'publication '  , 'preset.publication("'+s+'")'          ],
 
−
          [ 1, 'publication (with solvent)'  , 'preset.pub_solv("'+s+'")'          ],
 
−
          [ 0, ''              ,''                            ],                     
 
−
          [ 1, 'default'  ,'preset.default("'+s+'")'          ],         
 
−
          ]
 
−
 
−
#def hydrogens(s):
 
−
#  return [[ 2, 'Hydrogens:'      ,''                        ],   
 
−
#          [ 1, 'add'  ,'cmd.h_add("'+s+'")'          ],         
 
−
#          [ 1, 'remove'  ,'cmd.remove("('+s+') and hydro")'          ],
 
−
#          ]
 
−
 
−
def state(s):
 
−
  return [[ 2, 'State:'      ,''                        ],
 
−
          [ 1, 'freeze'  ,'cmd.set("state",cmd.get_state(),"'+s+'")'        ],
 
−
          [ 1, 'thaw'  ,'cmd.set("state",0,"'+s+'")'        ],         
 
−
          ]
 
−
 
 
−
def movement(s):
 
−
  return [[ 2, 'Movement:'      ,''                        ],   
 
−
          [ 1, 'protect'  ,'cmd.protect("'+s+'")'          ],
 
−
          [ 1, 'deprotect'  ,'cmd.deprotect("'+s+'")'          ],         
 
−
          ]
 
−
 
 
−
def selection(s):
 
−
  return [[ 2, 'Selection:'      ,''                        ],   
 
−
          [ 1, 'mask'  ,'cmd.mask("'+s+'")'          ],
 
−
          [ 1, 'unmask'  ,'cmd.unmask("'+s+'")'          ],         
 
−
          ]
 
−
 
−
def compute(s):
 
−
  return [[ 2, 'Compute:'      ,''                        ],   
 
−
          [ 1, 'atom count'  ,'cmd.count_atoms("'+s+'",quiet=0)'          ],
 
−
          [ 0, ''              ,''                            ],         
 
−
          [ 1, 'formal charge sum'  ,'util.sum_formal_charges("'+s+'",quiet=0)'          ],
 
−
          [ 1, 'partial charges sum'  ,'util.sum_partial_charges("'+s+'",quiet=0)'          ],                     
 
−
          ]
 
−
 
−
def vacuum(s):
 
−
  return [[ 2, 'Vacuum Electrostatics:'      ,''                        ],
 
−
          [ 2, '\\955WARNING:\\595 Unvalidated and experimental code!', '' ],
 
−
          [ 1, 'protein surface potential (absolute)', 'util.protein_vacuum_esp("'+s+'",quiet=0)'          ],
 
−
          [ 1, 'protein surface potential (relative)', 'util.protein_vacuum_esp("'+s+'",absolute=0,quiet=0)'          ],
 
−
          [ 2, '\\955NOTE:\\559 Due to absence of solvent dielectric', ''],
 
−
          [ 2, '\\559"screening", vacuum electrostatic potentials', ''],
 
−
          [ 2, '\\559for macromolecules are only qualitatively', ''],
 
−
          [ 2, '\\559meaningful.  Please view with skepticism!', '' ],
 
−
          ]
 
−
 
 
−
def mol_assign(s):
 
−
  return [[ 2, 'Assign:'      ,''                        ],   
 
−
          [ 1, 'Amber 99 atomic properties',  'util.assign_amber99("'+s+'")' ],
 
−
          ]
 
−
 
 
−
def mol_generate(s):
 
−
  return [[ 2, 'Generate:'      ,''                        ],
 
−
          [ 1, 'vacuum electrostatics', vacuum(s) ],         
 
−
#          [ 1, 'assign', mol_assign(s) ],
 
−
          ]
 
−
 
 
−
def invert(s):
 
−
  return [[ 2, 'Invert:'      ,''                        ],   
 
−
          [ 1, 'within object(s)'    ,'cmd.select("'+s+'","((byobj '+s+') and not '+s+')",show=1)'    ],
 
−
          [ 1, 'within segments(s)'    ,'cmd.select("'+s+'","((byseg '+s+') and not '+s+')",show=1)'    ],         
 
−
          [ 1, 'within chains(s)'    ,'cmd.select("'+s+'","((bychain '+s+') and not '+s+')",show=1)'    ],
 
−
          [ 1, 'within residues(s)'  ,'cmd.select("'+s+'","((byres '+s+') and not '+s+')",show=1)'    ],                     
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'within molecule(s)'    ,'cmd.select("'+s+'","((bymol '+s+') and not '+s+')",show=1)'    ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'within any'    ,'cmd.select("'+s+'","(not '+s+')",show=1)'    ],
 
−
          ]
 
−
 
−
def complete(s):
 
−
  return [[ 2, 'Complete:'      ,''                        ],   
 
−
 
−
          [ 1, 'resides'  ,'cmd.select("'+s+'","(byres '+s+')",show=1)'      ],
 
−
          [ 1, 'chains'  ,'cmd.select("'+s+'","(bychain '+s+')",show=1)'      ],
 
−
          [ 1, 'segments'  ,'cmd.select("'+s+'","(byseg '+s+')",show=1)'      ],
 
−
          [ 1, 'objects'  ,'cmd.select("'+s+'","(byobj '+s+')",show=1)'      ],
 
−
          [ 0, ''              ,''                            ],         
 
−
          [ 1, 'molecules'  ,'cmd.select("'+s+'","(bymol '+s+')",show=1)'      ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'C-alphas'  ,'cmd.select("'+s+'","(bycalpha '+s+')",show=1)'      ],         
 
−
          ]
 
−
 
−
def expand(s):
 
−
  return [[ 2, 'Expand:'      ,''                        ],   
 
−
          [ 1, 'by 4 A'  ,'cmd.select("'+s+'","('+s+' expand 4)",show=1)' ],
 
−
          [ 1, 'by 6 A'  ,'cmd.select("'+s+'","('+s+' expand 6)",show=1)' ],         
 
−
          [ 1, 'by 8 A'  ,'cmd.select("'+s+'","('+s+' expand 8)",show=1)' ],
 
−
          [ 1, 'by 12 A'  ,'cmd.select("'+s+'","('+s+' expand 12)",show=1)' ],
 
−
          [ 1, 'by 16 A'  ,'cmd.select("'+s+'","('+s+' expand 16)",show=1)' ],
 
−
          [ 1, 'by 20 A'  ,'cmd.select("'+s+'","('+s+' expand 20)",show=1)' ],         
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'by 4 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 4))",show=1)' ],
 
−
          [ 1, 'by 6 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 6))",show=1)' ],
 
−
          [ 1, 'by 8 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 8))",show=1)' ],
 
−
          [ 1, 'by 12 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 12))",show=1)' ],
 
−
          [ 1, 'by 16 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 16))",show=1)' ],
 
−
          [ 1, 'by 20 A, residues'  ,'cmd.select("'+s+'","(byres ('+s+' expand 20))",show=1)' ],
 
−
          ]
 
−
 
−
def around(s):
 
−
  return [[ 2, 'Around:'      ,''                        ],   
 
−
          [ 1, 'atoms within 4 A'  ,'cmd.select("'+s+'","('+s+' around 4)",show=1)' ],
 
−
          [ 1, 'atoms within 6 A'  ,'cmd.select("'+s+'","('+s+' around 6)",show=1)' ],         
 
−
          [ 1, 'atoms within 8 A'  ,'cmd.select("'+s+'","('+s+' around 8)",show=1)' ],
 
−
          [ 1, 'atoms within 12 A'  ,'cmd.select("'+s+'","('+s+' around 12)",show=1)' ],
 
−
          [ 1, 'atoms within 16 A'  ,'cmd.select("'+s+'","('+s+' around 16)",show=1)' ],
 
−
          [ 1, 'atoms within 20 A'  ,'cmd.select("'+s+'","('+s+' around 20)",show=1)' ],                     
 
−
          [ 0, ''              ,''                            ],         
 
−
          [ 1, 'residues within 4 A'  ,'cmd.select("'+s+'","(byres ('+s+' around 4))",show=1)' ],
 
−
          [ 1, 'residues within 6 A'  ,'cmd.select("'+s+'","(byres ('+s+' around 6))",show=1)' ],
 
−
          [ 1, 'residues within 8 A'  ,'cmd.select("'+s+'","(byres ('+s+' around 8))",show=1)' ],
 
−
          [ 1, 'residues within 16 A'  ,'cmd.select("'+s+'","(byres ('+s+' around 12))",show=1)' ],
 
−
          [ 1, 'residues within 20 A'  ,'cmd.select("'+s+'","(byres ('+s+' around 20))",show=1)' ],                               
 
−
          ]
 
−
 
 
−
def extend(s):
 
−
  return [[ 2, 'Extend:'      ,''                        ],   
 
−
          [ 1, 'by 1 bond'  ,'cmd.select("'+s+'","('+s+' extend 1)",show=1)' ],
 
−
          [ 1, 'by 2 bonds'  ,'cmd.select("'+s+'","('+s+' extend 2)",show=1)' ],         
 
−
          [ 1, 'by 3 bonds'  ,'cmd.select("'+s+'","('+s+' extend 3)",show=1)' ],
 
−
          [ 1, 'by 4 bonds'  ,'cmd.select("'+s+'","('+s+' extend 4)",show=1)' ],
 
−
          [ 1, 'by 5 bonds'  ,'cmd.select("'+s+'","('+s+' extend 5)",show=1)' ],
 
−
          [ 1, 'by 6 bonds'  ,'cmd.select("'+s+'","('+s+' extend 6)",show=1)' ],         
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'by 1 bond, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 1))",show=1)' ],
 
−
          [ 1, 'by 2 bonds, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 2))",show=1)' ],
 
−
          [ 1, 'by 3 bonds, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 3))",show=1)' ],
 
−
          [ 1, 'by 4 bonds, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 4))",show=1)' ],
 
−
          [ 1, 'by 5 bonds, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 5))",show=1)' ],
 
−
          [ 1, 'by 6 bonds, residues'  ,'cmd.select("'+s+'","(byres ('+s+' extend 6))",show=1)' ],
 
−
          ]
 
−
 
−
def sele_action(s):
 
−
  return [[ 2, 'Actions:'      ,''                        ],   
 
−
          [ 1, 'delete selection', 'cmd.delete("'+s+'")'          ],
 
−
          [ 1, 'rename selection', 'cmd.wizard("renaming","'+s+'")'          ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'zoom'          ,'cmd.zoom("'+s+'")'            ],
 
−
          [ 1, 'center'        ,'cmd.center("'+s+'")'            ],         
 
−
          [ 1, 'origin'        ,'cmd.origin("'+s+'")'          ],
 
−
          [ 1, 'orient'        ,'cmd.orient("'+s+'")'          ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'preset'        ,presets(s)        ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'remove atoms'  ,'cmd.remove("'+s+'");cmd.delete("'+s+'")'          ],
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'around'        , around(s)        ],         
 
−
          [ 1, 'expand'        , expand(s)        ],
 
−
          [ 1, 'extend'        , extend(s)        ],
 
−
          [ 1, 'invert'        , invert(s)        ],
 
−
          [ 1, 'complete'      , complete(s)        ],
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'duplicate selection'      ,'cmd.select("'+s+'")'          ],
 
−
          [ 1, 'create object'  ,'cmd.create(None,"'+s+'")'    ],         
 
−
          [ 1, 'find polar contacts'  ,
 
−
            'cmd.dist("'+s+'_polar_conts","'+s+'","'+s+'",quiet=1,mode=2,labels=0)'
 
−
            ],                     
 
−
          [ 0, ''          ,''                                  ],
 
−
          [ 1, 'selection'      , selection(s)        ],         
 
−
          [ 1, 'movement'      , movement(s)        ],
 
−
          [ 1, 'compute'        , compute(s)        ],         
 
−
          ]
 
−
 
−
 
−
def mol_action(s):
 
−
  return [[ 2, 'Actions:'    , ''                      ],   
 
−
          [ 1, 'zoom'        , 'cmd.zoom("'+s+'")'      ],
 
−
          [ 1, 'center'        ,'cmd.center("'+s+'")'            ],
 
−
          [ 1, 'origin'      , 'cmd.origin("'+s+'")'    ],
 
−
          [ 1, 'orient'      , 'cmd.orient("'+s+'")'    ],
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'preset'  , presets(s)      ],
 
−
          [ 0, ''          ,''                                              ],         
 
−
          [ 1, 'generate'  , mol_generate(s)      ],         
 
−
          [ 0, ''              ,''                            ],
 
−
          [ 1, 'assign sec. struc.'  ,'cmd.dss("'+s+'")'        ],
 
−
          [ 1, 'find polar contacts'  ,
 
−
            'cmd.dist("'+s+'_polar_conts","'+s+'","'+s+'",quiet=1,mode=2,labels=0)'
 
−
            ],                     
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'rename object', 'cmd.wizard("renaming","'+s+'")'          ],
 
−
          [ 1, 'duplicate object'    ,'cmd.create(None,"'+s+'")'    ],         
 
−
          [ 1, 'delete object'      , 'cmd.delete("'+s+'")'    ],
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'add hydrogens'  ,'cmd.h_add("'+s+'")'    ],         
 
−
          [ 1, 'remove hydrogens'  ,'cmd.remove("(hydro and ('+s+'))")'    ],         
 
−
          [ 1, 'remove waters'  ,'cmd.remove("(resn HOH+WAT and ('+s+'))")'    ],
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'state'      , state(s)        ],                     
 
−
          [ 1, 'selection'      , selection(s)        ],         
 
−
          [ 1, 'movement'      , movement(s)        ],         
 
−
          [ 1, 'compute'        , compute(s)        ],
 
−
          ]
 
−
 
−
def simple_action(s):
 
−
  return [[ 2, 'Actions:'    , ''                      ],
 
−
          [ 1, 'zoom'        , 'cmd.zoom("'+s+'")'      ],
 
−
          [ 1, 'center'      , 'cmd.center("'+s+'")'    ],         
 
−
          [ 1, 'origin'      , 'cmd.origin("'+s+'")'    ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'delete'      , 'cmd.delete("'+s+'")'    ],
 
−
          ]
 
−
 
−
def test1(s):
 
−
      return [[ 2, 'Test1:'    , ''                      ],   
 
−
          [ 1, 'zoom'        , 'cmd.zoom("all")'    ],
 
−
          [ 1, 'center'  , 'cmd.center("all")'  ],         
 
−
          [ 1, 'origin'  , 'cmd.origin("all")'  ],
 
−
          ]
 
−
 
−
def test2(s):
 
−
      return [[ 2, 'Test2:'    , ''                      ],   
 
−
          [ 1, 'zoom'        , 'cmd.zoom("all")'    ],
 
−
          [ 1, 'center'  , 'cmd.center("all")'  ],         
 
−
          [ 1, 'origin'  , 'cmd.origin("all")'  ],
 
−
          ]
 
−
 
−
def all_action(s):
 
−
  return [[ 2, 'Actions:'    , ''                      ],   
 
−
          [ 1, 'zoom'        , 'cmd.zoom("all")'    ],
 
−
          [ 1, 'center'  , 'cmd.center("all")'  ],         
 
−
          [ 1, 'origin'  , 'cmd.origin("all")'  ],
 
−
          [ 0, ''            , ''                      ],         
 
−
          [ 1, 'preset'  , presets(s)    ],         
 
−
          [ 0, ''            , ''                      ],         
 
−
          [ 1, 'delete everything'  , 'cmd.delete("all")'    ],         
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'add hydrogens' ,'cmd.h_add("'+s+'")'    ],         
 
−
          [ 1, 'remove hydrogens'  ,'cmd.remove("(elem h and ('+s+'))")'    ],
 
−
          [ 1, 'remove waters'  ,'cmd.remove("(resn HOH+WAT and ('+s+'))")'    ],                     
 
−
          [ 0, ''          ,''                                              ],
 
−
          [ 1, 'selection'      , selection(s)        ],                     
 
−
          [ 1, 'movement'      , movement(s)        ],
 
−
          [ 1, 'compute'        , compute(s)        ],                     
 
−
          ]
 
−
 
−
 
−
def mol_labels(s):
 
−
  return [[ 2, 'Labels:'        , ''                                  ],
 
−
          [ 1, 'clear'          , 'cmd.label("'+s+'","\'\'")'        ],
 
−
          [ 0, ''              , ''                                  ],
 
−
          [ 1, 'residues'      ,
 
−
  """cmd.label('''(name ca+C1*+C1' and (byres("""+s+""")))''','''"%s-%s"%(resn,resi)''')"""  ],
 
−
          [ 1, 'chains'      ,  'util.label_chains("'+s+'")'  ],
 
−
          [ 1, 'segments'      ,  'util.label_segments("'+s+'")'  ],         
 
−
          [ 0, ''              , ''                                  ],         
 
−
          [ 1, 'atom name'      , 'cmd.label("'+s+'","name")'        ],
 
−
          [ 1, 'element symbol' , 'cmd.label("'+s+'","elem")'        ],         
 
−
          [ 1, 'residue name'  , 'cmd.label("'+s+'","resn")'        ],
 
−
          [ 1, 'residue identifier'    , 'cmd.label("'+s+'","resi")'        ],
 
−
          [ 1, 'chain identifier' , 'cmd.label("'+s+'","chain")'        ],
 
−
          [ 1, 'segment identifier'      , 'cmd.label("'+s+'","segi")'        ],         
 
−
          [ 0, ''              , ''                                  ],
 
−
          [ 1, 'b-factor'      , 'cmd.label("'+s+'","\'%1.2f\'%b")'  ],
 
−
          [ 1, 'occupancy'      , 'cmd.label("'+s+'","\'%1.2f\'%q")'  ],
 
−
          [ 1, 'vdw radius'      , 'cmd.label("'+s+'","\'%1.2f\'%vdw")'  ],
 
−
          [ 0, ''              , ''                                  ],
 
−
          [ 1, 'partial charge(.2f)' ,           
 
−
  'cmd.label("'+s+'","\'%.2f\'%partial_charge")'                      ],
 
−
          [ 1, 'partial charge(.4f)' ,
 
−
  'cmd.label("'+s+'","\'%.4f\'%partial_charge")'                      ],
 
−
          [ 1, 'formal charge' ,
 
−
  'cmd.label("'+s+'","\'%d\'%formal_charge")'                      ],
 
−
          [ 1, 'bohr radius'      , 'cmd.label("'+s+'","\'%1.2f\'%bohr")'  ],                               
 
−
          [ 0, ''              , ''                                  ],
 
−
          [ 1, 'text type'      , 'cmd.label("'+s+'","text_type")'    ],
 
−
          [ 1, 'numeric type'  , 'cmd.label("'+s+'","numeric_type")' ],
 
−
          [ 0, ''              , ''                                  ],     
 
−
          [ 1, 'atom i.d.'            , 'cmd.label("'+s+'","id")' ],
 
−
          [ 1, 'atom i.d.(+1)'          , 'cmd.label("'+s+'","id+1")' ],
 
−
          ]
 
−
 
−
 
−
def mol_view(s):
 
−
  return [
 
−
      [ 1, 'zoom'          ,'cmd.zoom("'+s+'")'            ],
 
−
      [ 1, 'center'          ,'cmd.center("'+s+'")'            ],
 
−
      [ 1, 'origin'          ,'cmd.origin("'+s+'")'            ],
 
−
      [ 1, 'orient'          ,'cmd.orient("'+s+'")'            ],
 
−
      ]
 
−
 
−
def all_option(s):
 
−
  return [
 
−
      [ 2, '(all)'      , '' ],
 
−
      [ 1, 'show'      , mol_show(s) ],
 
−
      [ 1, 'hide'      , mol_hide(s) ],
 
−
      [ 1, 'color'      , mol_color(s) ],
 
−
      [ 1, 'view'      , mol_view(s) ],
 
−
      [ 1, 'preset'      , presets(s) ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'zoom'          ,'cmd.zoom("'+s+'")'            ],
 
−
      [ 1, 'center'          ,'cmd.center("'+s+'")'            ],
 
−
      [ 1, 'origin'          ,'cmd.origin("'+s+'")'            ],
 
−
      [ 1, 'orient'          ,'cmd.orient("'+s+'")'            ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'label'      , mol_labels(s) ],
 
−
      [ 0, '', '' ],
 
−
      [ 1, 'enable'        ,'cmd.enable("'+s+'")'            ],
 
−
      [ 1, 'disable'        ,'cmd.disable("'+s+'")'            ],
 
−
      ]
 
−
 
−
def enable_disable(enable):
 
−
  if enable:
 
−
      result = [[ 2, 'Enable', '' ]]
 
−
      cmmd = 'cmd.enable("'
 
−
  else:
 
−
      result = [[ 2, 'Disable', '']]
 
−
      cmmd = 'cmd.disable("'
 
−
  return result + map(lambda ob,cm=cmmd:[1,ob,cm+ob+'")'],['all']+cmd.get_names('objects'))
 
−
 
 
−
def main_menu():
 
−
  return [
 
−
      [ 2, 'Main Pop-Up'  , '' ],
 
−
      [ 1, 'zoom (vis)'          ,'cmd.zoom("visible")'            ],
 
−
      [ 1, 'center (vis)'          ,'cmd.center("visible")'            ],     
 
−
      [ 1, 'orient (vis)'          ,'cmd.orient("visible")'            ],
 
−
      [ 1, 'reset'          ,'cmd.reset()'            ],
 
−
      [ 0, ''            , ''                      ],         
 
−
      [ 1, '(all)'      , all_option("all") ],
 
−
      [ 1, '(visible)'      , all_option("visible") ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'ray'          ,'cmd.ray()' ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'enable', enable_disable(1) ],
 
−
      [ 1, 'disable', enable_disable(0) ], 
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'delete all'          ,'cmd.delete("all")' ],
 
−
      [ 1, 'reinitialize'          ,'cmd.reinitialize()' ],
 
−
      [ 1, 'quit'          ,'cmd.quit()' ],
 
−
      ]
 
−
 
−
def pick_option(title,s,object=0):
 
−
 
 
−
  result = [
 
−
      [ 2, title, '' ],
 
−
      [ 1, 'color'      , mol_color(s) ],
 
−
      [ 1, 'show'      , mol_show(s) ],
 
−
      [ 1, 'hide'      , mol_hide(s) ],
 
−
      [ 1, 'preset'  , presets(s)      ],     
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'zoom'          ,'cmd.zoom("'+s+'")'            ],
 
−
      [ 1, 'center'          ,'cmd.center("'+s+'")'            ],
 
−
      [ 1, 'origin'          ,'cmd.origin("'+s+'")'            ],
 
−
      [ 1, 'orient'          ,'cmd.orient("'+s+'")'            ],
 
−
      [ 1, 'indicate'        ,'cmd.indicate("'+s+'")'            ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'labels'      , mol_labels(s) ],
 
−
      ]
 
−
 
 
# Edit dwkulp 6/11/05 , add a rotamer menu to residue menu
 
# Edit dwkulp 6/11/05 , add a rotamer menu to residue menu
 
   if title == 'Residue':
 
   if title == 'Residue':
 
result.extend([[ 1, 'rotamers'    , rotamer_menu(s)]])
 
result.extend([[ 1, 'rotamers'    , rotamer_menu(s)]])
 +
</source>
  
−
  if object:
+
2. At the end of the file add this:
−
      result.extend([
+
<source lang="python">
−
        [ 0, ''            , ''                      ],       
 
−
        [ 1, 'disable'        ,'cmd.disable("'+s+'")'            ],
 
−
        [ 0, ''            , ''                      ],
 
−
        [ 1, 'delete'        ,'cmd.delete("'+s+'")'            ]       
 
−
        ])
 
−
  else:
 
−
      result.extend([
 
−
      [ 0, ''            , ''                      ],     
 
−
      [ 1, 'create object','cmd.create(None,"'+s+'")'            ],     
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'remove'      , 'cmd.remove("'+s+'")' ],   
 
−
                    ])
 
−
  return result
 
−
 
 
−
def pick_option_rev(title,s,object=0):
 
−
  result = pick_option(title,s,object)[1:]
 
−
  result.reverse()
 
−
  return result
 
−
 
 
−
def pick_menu(s1,s2):
 
−
  if s1[-1]=='`':
 
−
      title = s1[0:-1]
 
−
  else:
 
−
      title = s1
 
−
  return [[ 2, title    , '' ],
 
−
          [ 1, 'atom'    , pick_option("Atom",s2) ],
 
−
          [ 1, 'residue' , pick_option("Residue","(byres ("+s2+"))") ],
 
−
          [ 1, 'chain'  , pick_option("Chain","(bychain ("+s2+"))") ],
 
−
          [ 1, 'segment' , pick_option("Segment","(byseg ("+s2+"))") ],
 
−
          [ 1, 'object'  , pick_option("Object","(byobject ("+s2+"))",1) ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'molecule', pick_option("Molecule","(bymol ("+s2+"))") ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'fragment', pick_option("Fragment","(byfrag ("+s2+"))") ],
 
−
          [ 1, 'fragment+joint(s)', pick_option("Fragment","((byfrag ("+s2+")) extend 1)") ],
 
−
          ]
 
−
     
 
−
def seq_menu(s2,s3):
 
−
 
 
−
  return [[ 2, 'Sequence'    , '' ],
 
−
          [ 1, 'selection', pick_option('('+s3+')',s3) ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'residue' , pick_option("Residue","(byres ("+s2+"))") ],
 
−
          [ 1, 'chain'  , pick_option("Chain","(bychain ("+s2+"))") ],
 
−
          [ 1, 'segment' , pick_option("Segment","(byseg ("+s2+"))") ],
 
−
          [ 1, 'object'  , pick_option("Object","(byobject ("+s2+"))",1) ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'molecule', pick_option("Molecule","(bymol ("+s2+"))") ],
 
−
          [ 0, ''            , ''                      ],
 
−
          [ 1, 'C-alpha'    , pick_option("C-alpha",s2) ],
 
−
          ]
 
−
     
 
−
 
 
−
def seq_option(title,s,object=0):
 
−
  c=len(title)-1
 
−
  while title[c]!='/':
 
−
      c = c-1
 
−
  title = title[0:c+1]
 
−
 
 
−
  result = [
 
−
      [ 2, title, '' ],
 
−
      [ 1, 'color'      , mol_color(s) ],
 
−
      [ 1, 'show'      , mol_show(s) ],
 
−
      [ 1, 'hide'      , mol_hide(s) ],
 
−
      [ 1, 'preset'  , presets(s)      ],     
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'zoom'          ,'cmd.zoom("'+s+'")'            ],
 
−
      [ 1, 'center'          ,'cmd.center("'+s+'")'            ],
 
−
      [ 1, 'origin'          ,'cmd.origin("'+s+'")'            ],
 
−
      [ 1, 'orient'          ,'cmd.orient("'+s+'")'            ],
 
−
      [ 1, 'indicate'        ,'cmd.indicate("'+s+'")'            ],
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'labels'      , mol_labels(s) ],
 
−
 
 
−
 
 
−
      ]
 
−
 
 
−
  if object:
 
−
      result.extend([
 
−
        [ 0, ''            , ''                      ],       
 
−
        [ 1, 'disable'        ,'cmd.disable("'+s+'")'            ],
 
−
        [ 0, ''            , ''                      ],
 
−
        [ 1, 'delete'        ,'cmd.delete("'+s+'")'            ]       
 
−
        ])
 
−
  else:
 
−
      result.extend([
 
−
      [ 0, ''            , ''                      ],     
 
−
      [ 1, 'create object','cmd.create(None,"'+s+'")'            ],           
 
−
      [ 0, ''            , ''                      ],
 
−
      [ 1, 'remove'      , 'cmd.remove("'+s+'")' ],   
 
−
                    ])
 
−
  return result
 
−
 
 
−
 
 
 
###############################################
 
###############################################
 
# Dan Kulp
 
# Dan Kulp
Line 1,078: Line 492:
 
# Check for rotamer library being loaded
 
# Check for rotamer library being loaded
 
if not rotamers.rotdat:
 
if not rotamers.rotdat:
−
    return [ [2, "Must run rotamers.py first",'']]
+
            rotamers.readRotLib()
 +
#     return [ [2, "Must run rotamers.py first",'']]
  
 
# Check for valid rotamer residue..
 
# Check for valid rotamer residue..
Line 1,095: Line 510:
  
 
# Set max number of rotamers to display (probably should be somewhere 'higher up' in the code)
 
# Set max number of rotamers to display (probably should be somewhere 'higher up' in the code)
−
max_rotamers = 10
+
max_rotamers = min(10, len(match_rotamers))
−
 
 
−
 
 
−
if len(match_rotamers) < max_rotamers:
 
−
    max_rotamers = len(match_rotamers)
 
  
 
# Create menu entry for each possible rotamer
 
# Create menu entry for each possible rotamer
−
         for item in range(0,max_rotamers):
+
         for item in range(max_rotamers):
 
             result.append( [ 1, str(match_rotamers[item]), 'rotamers.set_rotamer("'+s+'","'\
 
             result.append( [ 1, str(match_rotamers[item]), 'rotamers.set_rotamer("'+s+'","'\
 
    +str(match_rotamers[item][1])+'","'\
 
    +str(match_rotamers[item][1])+'","'\
Line 1,109: Line 520:
 
    +str(match_rotamers[item][4])+'")'])
 
    +str(match_rotamers[item][4])+'")'])
 
return result
 
return result
 +
  
 
</source>
 
</source>
Line 1,114: Line 526:
  
 
[[Category:Script_Library|Rotamer Toggle]]
 
[[Category:Script_Library|Rotamer Toggle]]
 +
 +
[[Category:Structural_Biology_Scripts|Rotamer Toggle]]

Latest revision as of 04:04, 17 August 2010

DESCRIPTION

Backbone-Dependent Rotamer library (Dunbrack, Cohen ; see ref) is imported into pymol giving access to this information. There are a number of different ways to use the data, I've only implemented a few as well as added extra functions that seemed useful.

  • Rotamer Menu - an added menu into menu.py, which displays the most common rotamers for the given(clicked) residue; you can also set the residue any of the common rotamers as well
  • colorRotamers - color rotamers by closest matching rotamer angles from database; i.e. color by how common each rotamer of selection, blue - red (least to most common).
  • set_rotamer - routine called by above menu, but can be called manually to set a specific residues side-chain angles
  • set_phipsi - set all phi,psi angles of given selection to given angles (useful for creating secondary structures)
  • createRotamerPDBs - create pdb for each rotamer of given selection ; filter by rotamer-probability

IMAGES

  • Rotamer Menu for a GLN residue

  • Rotamer Comparison of crystal structure and most common for GLU; just as an example

Print out while selecting most common rotamer from above-left image (GLN residue): 

 Given GLN:40 PHI,PSI (-171.626373291,-96.0500335693) : bin (-170,-100)
 CHIs: [179.18069458007812, 72.539344787597656, -47.217315673828125]
 Setting Chi1 to -176.9
 Setting Chi2 to 177.4
 Setting Chi3 to 0.7

SETUP

run "rotamers.py" and use functions from commandline.

or

To setup a rotamer menu inside the residue menu (default windows pymol installation):

  • copy rotamers.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/rotamers.py
  • copy mymenu.py to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/menu.py (WARNING : overwrites default menu.py - use at your own risk)
  • copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep)

This is only one possible way to do this, I am sure there are many others. I'm not going to post the bbdep, but there is a link in the References section to Dunbrack's download page (get the "sorted" lib)

NOTES / STATUS

  • Tested on Pymolv0.97, Windows platform, Red Hat Linux 9.0 and Fedora Core 4. Will test v0.98 and MacOSX later on.
  • The way it's setup now, when you import rotamers , it will automatically read-in the rotamer database; this may not be what you want.
  • Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu

TASKS TODO:

  • Rotamer Movie, using mset, etc create movie to watch cycle through rotamers
  • Code could be organized a bit better; due to time constraints this is good for now..

TASKS DONE:

  • Store crystal structure in rotamer menu, so you can go back to original orientation

USAGE

colorRotamers selection
set_rotamer selection, chi1_angle [,chi2_angle] [,chi3_angle] [,chi4_angle]
set_phipsi selection phi_angle, psi_angle
createRotamerPBDs selection [,ncutoff] [,pcutoff] [,prefix]

EXAMPLES

  colorRotamers chain A
  set_rotamer resi 40, -60,-40   (only set chi1,chi2 angles)
  set_phipsi resi 10-40, -60,-60 (create an alpha-helical-like section)
  createRotamerPDBs resi 10-12, ncutoff=3 (create 9 PDBs; each with one of the 3 most probable rotamers for resi 10,11,12)
  createRotamerPDBs resi 14, pcutoff=0.4  (create a pdb file for each rotamer of residue 14 with probablity > 0.4)

REFERENCES

Dunbrack and Cohen. Protein Science 1997

Dunbrack Lab Page (Contains backbone-dependent library)

SCRIPTS (Rotamers.py ; MyMenu.py)

Rotamers.py 

##################################################################
# File:          Rotamers.py
# Author:        Dan Kulp
# Creation Date: 6/8/05
# Contact:       dwkulp@mail.med.upenn.edu
#
# Notes:
#     Incorporation of Rotamer library
#     readRotLib() - fills rotdat; 
#        indexed by "RES:PHI_BIN:PSI_BIN".
#
#     Three main functions:
#     1. colorRotamers - colors according
#          to rotamer probablitity
#     2. getBins(sel)
#           phi,psi bin for rotamer
#     3. set_rotamer - set a side-chain 
#           to a specific rotamer
#
#     To setup a rotamer menu in the 
#   right click, under "Residue"
#        1. cp mymenu.py modules/pymol/menu.py
#        2. cp rotamers.py modules/pymol/rotamers.py (update ROTLIB)
#
# Requirements:
#  set ROTLIB to path for rotamer library
# Reference: 
#  Dunbrack and Cohen. Protein Science 1997
####################################################################
 
import colorsys,sys
import editing
import os
import cmd
import math
 
# Path for library
ROTLIB=os.environ['PYMOL_PATH']+"/modules/pymol/bbdep02.May.sortlib"
 
# Place for library in memory..
rotdat = {}
 
def readRotLib():
    # Column indexes in rotamer library..
    RES  = 0
    PHI  = 1
    PSI  = 2
    PROB = 8
    CHI1 = 9
    CHI2 = 10
    CHI3 = 11
    CHI4 = 12
 
    if os.path.exists(ROTLIB):
                print "File exists: "+ROTLIB
                input = open(ROTLIB, 'r')
                for line in input:
 
                    # Parse by whitespace (I believe format is white space and not fixed-width columns)
                    dat = line.split()
 
                    # Add to rotamer library in memory : 
                    #   key format       RES:PHI_BIN:PSI_BIN
                    #   value format     PROB, CHI1, CHI2, CHI3, CHI4
                    key=dat[RES]+":"+dat[PHI]+":"+dat[PSI]
                    if key in rotdat:
                        rotdat[key].append([ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ])
                    else:
                        rotdat[key] = [ [ dat[PROB], dat[CHI1], dat[CHI2], dat[CHI3], dat[CHI4] ] ]
 
 
    else:
        print "Couldn't find Rotamer library"
 
 
# Atoms for each side-chain angle for each residue
CHIS = {}
CHIS["ARG"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD" ],
                ["CB","CG","CD","NE" ],
                ["CG","CD","NE","CZ" ]
              ]
 
CHIS["ASN"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","OD2" ]
              ]
 
CHIS["ASP"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","OD1" ]
              ]
CHIS["CYS"] = [ ["N","CA","CB","SG" ]
              ]
 
CHIS["GLN"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD" ],
                ["CB","CG","CD","OE1"]
              ]
 
CHIS["GLU"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD" ],
                ["CB","CG","CD","OE1"]
              ]
 
CHIS["HIS"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","ND1"]
              ]
 
CHIS["ILE"] = [ ["N","CA","CB","CG1" ],
                ["CA","CB","CG1","CD1" ]
              ]
 
CHIS["LEU"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD1" ]
              ]
 
CHIS["LYS"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD" ],
                ["CB","CG","CD","CE"],
                ["CG","CD","CE","NZ"]
              ]
 
CHIS["MET"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","SD" ],
                ["CB","CG","SD","CE"]
              ]
 
CHIS["PHE"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD1" ]
              ]
 
CHIS["PRO"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD" ]
              ]
 
CHIS["SER"] = [ ["N","CA","CB","OG" ]
              ]
 
CHIS["THR"] = [ ["N","CA","CB","OG1" ]
              ]
 
CHIS["TRP"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD1"]
              ]
 
CHIS["TYR"] = [ ["N","CA","CB","CG" ],
                ["CA","CB","CG","CD1" ]
              ]
 
CHIS["VAL"] = [ ["N","CA","CB","CG1" ]
              ]
 
# Color Rotamer by side-chain angle position
#  'bin' side-chain angles into closest
def colorRotamers(sel):
    doRotamers(sel)
 
# Utility function, to set phi,psi angles for a given selection
# Note: Cartoon, Ribbon functionality will not display correctly after this
def set_phipsi(sel, phi,psi):
    doRotamers(sel,angles=[phi,psi],type="set")
 
# Set a rotamer, based on a selection, a restype and chi angles
def set_rotamer(sel, chi1, chi2=0,chi3=0,chi4=0):
    at = cmd.get_model("byres ("+sel+")").atom[0]
 
    list = [chi1,chi2,chi3,chi4]
    for i in range(len(CHIS[at.resn])):
        print "Setting Chi"+str(i+1)+" to "+str(list[i])
        editing.set_dihedral(sel + ' and name '+CHIS[at.resn][i][0],
                             sel + ' and name '+CHIS[at.resn][i][1],
                             sel + ' and name '+CHIS[at.resn][i][2],
                             sel + ' and name '+CHIS[at.resn][i][3], str(list[i]))
 
    # Remove some objects that got created
    cmd.delete("pk1")
    cmd.delete("pk2")
    cmd.delete("pkmol")
 
# Get Phi,Psi bins for given selection
# WARNING:  assume selection is single residue (will only return first residue bins)
def getBins(sel):
    return doRotamers(sel, type="bins")
 
# Color Ramp...
def rot_color(vals): 
        nbins = 10
        vals.sort(key=lambda x:x[1])
#       print "End sort: "+str(len(vals))+" : "+str(nbins)
 
 
        # Coloring scheme...
        j = 0
        rgb = [0.0,0.0,0.0]
        sel_str = ""
        for i in range(len(vals)):
                if int(len(vals)/nbins) == 0 or i % int(len(vals)/nbins) == 0:
                      hsv = (colorsys.TWO_THIRD - colorsys.TWO_THIRD * float(j) / (nbins-1), 1.0, 1.0)
 
                      #convert to rgb and append to color list
                      rgb = colorsys.hsv_to_rgb(hsv[0],hsv[1],hsv[2])
                      if j < nbins-1:
                              j += 1
 
                cmd.set_color("RotProbColor"+str(i), rgb)
                cmd.color("RotProbColor"+str(i), str(vals[i][0]))
 
 
# Main function
def doRotamers(sel,angles=[], type="color"):
 
        # Read in Rotamer library if not already done
        if len(rotdat) == 0:
                readRotLib()
 
        # Set up some variables..
        residues = ['dummy']  # Keep track of residues already done
        probs = []            # probability of each residue conformation
        phi = 0               # phi,psi angles of current residue
        psi = 0
 
        # Get atoms from selection
        atoms = cmd.get_model("byres ("+sel+")")
 
        # Loop through atoms in selection
        for at in atoms.atom:
            try:
               # Don't process Glycines or Alanines
               if not (at.resn == 'GLY' or at.resn == 'ALA'):
                if at.chain+":"+at.resn+":"+at.resi not in residues:
                    residues.append(at.chain+":"+at.resn+":"+at.resi)
 
                    # Check for a null chain id (some PDBs contain this) 
                    unit_select = ""
                    if at.chain != "":
                        unit_select = "chain "+str(at.chain)+" and "
 
                    # Define selections for residue i-1, i and i+1
                    residue_def = unit_select+'resi '+str(at.resi)
                    residue_def_prev = unit_select+'resi '+str(int(at.resi)-1)
                    residue_def_next = unit_select+'resi '+str(int(at.resi)+1)
 
                    # Compute phi/psi angle
 
                    phi = cmd.get_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C')
                    psi = cmd.get_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N')
                    if type == "set":
                            print "Changing "+at.resn+str(at.resi)+" from "+str(phi)+","+str(psi)+" to "+str(angles[0])+","+str(angles[1])
                            cmd.set_dihedral(residue_def_prev+' and name C',residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',angles[0])
                            cmd.set_dihedral(residue_def+' and name N',residue_def+' and name CA',residue_def+' and name C',residue_def_next+' and name N', angles[1])
                            continue
 
                    # Find correct 10x10 degree bin                                     
                    phi_digit = abs(int(phi)) - abs(int(phi/10)*10)
                    psi_digit = abs(int(psi)) - abs(int(psi/10)*10)
 
                    # Remember sign of phi,psi angles
                    phi_sign = 1
                    if phi < 0:    phi_sign = -1
 
                    psi_sign = 1
                    if psi < 0:    psi_sign = -1
 
                    # Compute phi,psi bins
                    phi_bin = int(math.floor(abs(phi/10))*10*phi_sign)
                    if phi_digit >= 5:    phi_bin = int(math.ceil(abs(phi/10))*10*phi_sign)
 
                    psi_bin = int(math.floor(abs(psi/10))*10*psi_sign)
                    if psi_digit >= 5:    psi_bin = int(math.ceil(abs(psi/10))*10*psi_sign)
 
                    print "Given "+at.resn+":"+at.resi+" PHI,PSI ("+str(phi)+","+str(psi)+") : bin ("+str(phi_bin)+","+str(psi_bin)+")"
 
 
                    # Get current chi angle measurements
                    chi = []
                    for i in range(len(CHIS[at.resn])):
                       chi.append(cmd.get_dihedral(residue_def + ' and name '+CHIS[at.resn][i][0],
                                                     residue_def + ' and name '+CHIS[at.resn][i][1],
                                                     residue_def + ' and name '+CHIS[at.resn][i][2],
                                                     residue_def + ' and name '+CHIS[at.resn][i][3]))
                    print "CHIs: "+str(chi)
                    if type == 'bins':
                         return [at.resn, phi_bin,psi_bin]
 
                    # Compute probabilities for given chi angles
                    prob = 0
                    prob_box = 22                   
                    for item in range(len(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)])):
                        print "Rotamer from db: "+str(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item])
                        if chi[0]:
                            if chi[0] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) - (prob_box/2) and \
                                chi[0] <= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][1]) + (prob_box/2):
                                if len(chi) == 1:
                                        prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
                                        break
                                if chi[1] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) - (prob_box/2) and \
                                 float(chi[1] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][2]) + (prob_box/2):
                                        if len(chi) == 2:
                                            prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
                                            break
                                        if chi[2] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) - (prob_box/2) and \
                                           float(chi[2] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][3]) + (prob_box/2):
                                            if len(chi) == 3:
                                                prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
                                                break
                                            if chi[3] >= float(rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) - (prob_box/2) and \
                                               float(chi[3] <= rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][4]) + (prob_box/2):
                                                prob = rotdat[at.resn+":"+str(phi_bin)+":"+str(psi_bin)][item][0]
                                                break
 
 
                    print "PROB OF ROTAMER: "+str(prob)
                    print "---------------------------"
                    probs.append([residue_def, prob])
 
            except:
#               probs.append([residue_def, -1])
                print "Exception found"
                continue
 
        # Color according to rotamer probability
        rot_color(probs)
 
 
 
 
#  Create PDB files containing most probable rotamers
def createRotamerPDBs(sel,ncutoff=10,pcutoff=0,prefix="ROTAMER"):
 
        # Get atoms from selection
        atoms = cmd.get_model("byres ("+sel+")")
 
        # Set up some variables..
        residues = ['dummy']  # Keep track of residues already done
 
        # Loop through atoms in selection
        for at in atoms.atom:
                if at.resn in ('GLY','ALA') or "%s:%s:%s" % (at.chain,at.resn,at.resi) in residues:
                        continue
 
                # Add to residue list (keep track of which ones we've done)
                residues.append("%s:%s:%s" % (at.chain,at.resn,at.resi))
 
                # Check for a null chain id (some PDBs contain this)
                unit_select = ""
                if not at.chain == "":
                    unit_select = "chain "+str(at.chain)+" and "
 
                # Define selections for residue 
                residue_def = unit_select+'resi '+str(at.resi)
 
                # Get bin (phi,psi) definitions for this residue
                bin = doRotamers(residue_def, type='bins')
 
                # Store crystal angle
                crystal_angles = [0.0,0.0,0.0,0.0]
                for angle in range(3):
                        try:
                                crystal_angles[angle] = bin[3][angle]
                        except IndexError:
                                break
 
                # Retreive list of rotamers for this phi,psi bin + residue type
                match_rotamers = rotdat["%s:%s:%s" % (bin[0],str(bin[1]),str(bin[2]))]
 
                count = 0
                for item in range(len(match_rotamers)):
 
                        # Store probablity
                        prob = match_rotamers[item][0]
 
                        # Check cutoffs
                        if float(prob) <= float(pcutoff):
                                continue
 
                        if float(count) >= float(ncutoff):
                                break
 
                        # Increment count
                        count += 1
 
                        # Output to screen ...
                        print "Residue %s%s, rotamer %i, prob %s" % (str(at.resn),str(at.resi),int(item),str(prob))
 
                        # Set to new rotamer
                        set_rotamer(residue_def,match_rotamers[item][1],match_rotamers[item][2],match_rotamers[item][3],match_rotamers[item][4])                                                                                                
 
                        # Store in PDB file
                        cmd.save("%s_%s%s_%i_%s.pdb" % (prefix,str(at.resn),str(at.resi),int(item),str(prob)))
 
                        # Reset crystal angle
                        set_rotamer(residue_def,crystal_angles[0],crystal_angles[1],crystal_angles[2],crystal_angles[3])
 
# Uncommenting this is nice because it loads rotamer library upon startup
#  however, it slows the PyMOL loading process a lot
#  instead I've put this call into the menuing code..
# readRotLib()
 
cmd.extend('set_phipsi',set_phipsi)
cmd.extend('set_rotamer',set_rotamer)
cmd.extend('colorRotamers',colorRotamers)
cmd.extend('createRotamerPDBs',createRotamerPDBs)

MyMenu.py 

Since menu.py is copyrighted I can't post my edited version, but you can create it very simply by adding these two peices of code

1. In the "pick_option(title,s,object=0)" function of menu.py add the following code after the first "result =" statement 

# Edit dwkulp 6/11/05 , add a rotamer menu to residue menu
   if title == 'Residue':
	result.extend([[ 1, 'rotamers'    , rotamer_menu(s)]])

2. At the end of the file add this: 

###############################################
# Dan Kulp
# Added Rotamer list to residue menu..
# rotamer.py must be importable (I placed it in 
# the same directory as menu.py)
###############################################

import rotamers


def rotamer_menu(s):
	# Check for rotamer library being loaded
	if not rotamers.rotdat:
             rotamers.readRotLib()
#	     return [ [2, "Must run rotamers.py first",'']]

	# Check for valid rotamer residue..
	res = cmd.get_model("byres ("+s+")").atom[0].resn
        if not res in rotamers.CHIS.keys():
	    return [ [2, "Residue: "+res+" not known sidechain or does not have rotamers", '']]

	# Get PHI,PSI bins for rotamer (also prints out current phi,psi, chi1,chi2,chi3,chi4)
	bins = rotamers.doRotamers(s,type='bins')

	# Add a title to the menu
	result = [ [2, bins[0]+' Rotamers in bin ('+str(bins[1])+','+str(bins[2])+')','' ], [1, ':::PROB,CHI1,CHI2,CHI3,CHI4:::','']]

        # Grab the entries for this residue and phi,psi bins
	match_rotamers = rotamers.rotdat[bins[0]+":"+str(bins[1])+":"+str(bins[2])]

	# Set max number of rotamers to display (probably should be somewhere 'higher up' in the code)
	max_rotamers = min(10, len(match_rotamers))

	# Create menu entry for each possible rotamer
        for item in range(max_rotamers):
             result.append( [ 1, str(match_rotamers[item]), 'rotamers.set_rotamer("'+s+'","'\
										    +str(match_rotamers[item][1])+'","'\
										    +str(match_rotamers[item][2])+'","'\
										    +str(match_rotamers[item][3])+'","'\
										    +str(match_rotamers[item][4])+'")'])
	return result
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