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Difference between revisions of "Rotamer Toggle"

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In progress... checking/fixing a few minor details to make things more robust... I'll post it later tonight
+
===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===
 +
<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):
 +
*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
 +
 
 +
[http://dunbrack.fccc.edu/bbdep/index.php Dunbrack Lab Page (Contains backbone-dependent library)]
 +
 
 +
===SCRIPTS (Rotamers.py ; MyMenu.py)===
 +
Rotamers.py
 +
<source lang="python">
 +
##################################################################
 +
# 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)
 +
</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
 +
 
 +
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">
 +
# Edit dwkulp 6/11/05 , add a rotamer menu to residue menu
 +
  if title == 'Residue':
 +
result.extend([[ 1, 'rotamers'    , rotamer_menu(s)]])
 +
</source>
 +
 
 +
2. At the end of the file add this:
 +
<source lang="python">
 +
###############################################
 +
# 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
 +
 
 +
 
 +
</source>
  
−
Dan Kulp
 
  
 
[[Category:Script_Library|Rotamer Toggle]]
 
[[Category:Script_Library|Rotamer Toggle]]
 +
 +
[[Category:Structural_Biology_Scripts|Rotamer Toggle]]

Latest revision as of 03:49, 28 March 2014

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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