Rotamer Toggle: Difference between revisions

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*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).
*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===
===IMAGES===
[[Image:RotamerMenu.png|thumb|left|Rotamer Menu for a GLN residue]]
<gallery>
[[Image:GLURotamerComparison5.png|thumb|left|Rotamer Comparison of crystal structure and most common for GLU; just as an example]]
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):
Print out while selecting most common rotamer from above-left image (GLN residue):
Line 34: Line 21:


===SETUP===
===SETUP===
Simply "import rotamers" and use the functions manually.
run "rotamers.py" and use functions from commandline.


or
or
Line 43: Line 30:
*copy bbdep02.May.sortlib to C:/Program Files/DeLano Scientific/PyMol/modules/pymol/bbdep02.May.sortlib (or newer version of sorted bbdep)
*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)
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===
===NOTES / STATUS===
*Tested on Pymolv0.97, Windows platform and on Red Hat Linux 9.0. Will test v0.98 later on.
*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.
*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
*Post problems in the discussion page, on 'my talk' page or just email me : dwkulp@mail.med.upenn.edu
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  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 67: 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 93: 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 105: 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 130: 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","SG" ]
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" ],
CHIS["TRP"] = [ ["N","CA","CB","CG" ],
                 ["CA","CB","CG","CD1"]
                 ["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
MyMenu.py
Line 441: 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 458: 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 472: Line 520:
    +str(match_rotamers[item][4])+'")'])
    +str(match_rotamers[item][4])+'")'])
return result
return result


</source>
</source>

Latest revision as of 03:04, 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 Menu for a GLN residue

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

    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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