''' Described at PyMOL wiki: http://www.pymolwiki.org/index.php/colorbydisplacement --- ColorByRMSD: RMSD based coloring --- Authors : Shivender Shandilya; Jason Vertrees Program : ColorByRMSD Date : July 2009 http://www.pymolwiki.org/index.php/ColorByRMSD """ """ --- colorbydisplacement: Displacement based coloring --- Authors : Troels E. Linnet Program : colorbydisplacement Date : January 2011 """ """ colorbydisplacement -- Show the distance displacement deviation in color to more easily see variable regions. PARAMS objSel1 (valid PyMOL object or selection) The first object objSel2 (valid PyMOL object or selection) The second object doColor (boolean, either True or False) If doColor=True then a simple representation is created to highlight the differences. If False, then no changes are made. DEFAULT: False RETURNS None. SIDE-EFFECTS Modifies the B-factor columns in your original structures. ''' from __future__ import print_function from pymol import cmd from pymol import stored def strTrue(p): return p[0].upper() == "T" def displacementUpdateBAll(objA, alnAri, objB, alnBri): print("This will take a while to go through the for loops. Give me around 3-5 minutes...") # If residue is unassigned in one of the pdb files, we reset its value for x in range(len(alnAri)): s1 = objA + " and resi " + alnAri[x][0] + " and name " + str(alnAri[x][1]) cmd.alter(s1, "b = " + str(-0.01)) for x in range(len(alnBri)): s2 = objB + " and resi " + alnBri[x][0] + " and name " + alnBri[x][1] cmd.alter(s2, "b = " + str(-0.01)) cmd.sort(objA) cmd.sort(objB) for x in range(len(alnAri)): s1 = objA + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1] s2 = objB + " and resi " + alnAri[x][0] + " and name " + alnAri[x][1] # Names starting with __ (underscores) are normally hidden by PyMOL tempObject = "__tempObject" Displacement = cmd.distance(tempObject, s1, s2) cmd.alter(s1, "b = " + str(Displacement)) cmd.alter(s2, "b = " + str(Displacement)) cmd.delete(tempObject) cmd.sort(objA) cmd.sort(objB) def ColorByDisplacementAll(objSel1, objSel2, super1='all', super2='all', doColor="True", doAlign="True", AlignedWhite='yes'): # First create backup copies; names starting with __ (underscores) are normally hidden by PyMOL tObj1, tObj2, aln = "__tempObj1", "__tempObj2", "__aln" if strTrue(doAlign): # Create temp objects cmd.create(tObj1, objSel1) cmd.create(tObj2, objSel2) # Align and make create an object aln which indicates which atoms were paired between the two structures # Super is must faster than align http://www.pymolwiki.org/index.php/Super cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln) # Modify the original matrix of object1 from the alignment cmd.matrix_copy(tObj1, objSel1) else: # Create temp objects cmd.create(tObj1, objSel1) cmd.create(tObj2, objSel2) # Align and make create an object aln which indicates which atoms were paired between the two structures # Super is must faster than align http://www.pymolwiki.org/index.php/Super cmd.super(tObj1 + ' and ' + str(super1), tObj2 + ' and ' + str(super2), object=aln) # Modify the B-factor columns of the original objects, # in order to identify the residues NOT used for alignment, later on cmd.alter(objSel1 + " or " + objSel2, "b=-0.2") cmd.alter(tObj1 + " or " + tObj2, "chain='A'") cmd.alter(tObj1 + " or " + tObj2, "segi='A'") # Update pymol internal representations; one of these should do the trick cmd.refresh() cmd.rebuild() cmd.sort(tObj1) cmd.sort(tObj2) # Create lists for storage stored.alnAres, stored.alnBres = [], [] # Iterate over objects and get resi if AlignedWhite == 'yes': cmd.iterate(tObj1 + " and not " + aln, "stored.alnAres.append((resi, name))") cmd.iterate(tObj2 + " and not " + aln, "stored.alnBres.append((resi, name))") else: cmd.iterate(tObj1, "stored.alnAres.append((resi, name))") cmd.iterate(tObj2, "stored.alnBres.append((resi, name))") # Change the B-factors for EACH object displacementUpdateBAll(tObj1, stored.alnAres, tObj2, stored.alnBres) # Store the NEW B-factors stored.alnAnb, stored.alnBnb = [], [] # Iterate over objects and get b if AlignedWhite == 'yes': # Iterate over objects which is not aligned cmd.iterate(tObj1 + " and not " + aln, "stored.alnAnb.append(b)") cmd.iterate(tObj2 + " and not " + aln, "stored.alnBnb.append(b)") else: # Or Iterate over all objects with CA cmd.iterate(tObj1, "stored.alnAnb.append(b)") cmd.iterate(tObj2, "stored.alnBnb.append(b)") # Get rid of all intermediate objects and clean up cmd.delete(tObj1) cmd.delete(tObj2) cmd.delete(aln) # Assign the just stored NEW B-factors to the original objects print("Sooon ready. 1 more minute") for x in range(len(stored.alnAres)): cmd.alter(objSel1 + " and resi " + str(stored.alnAres[x][0]) + " and name " + str(stored.alnAres[x][1]), "b = " + str(stored.alnAnb[x])) for x in range(len(stored.alnBres)): cmd.alter(objSel2 + " and resi " + str(stored.alnBres[x][0]) + " and name " + str(stored.alnBres[x][1]), "b = " + str(stored.alnBnb[x])) cmd.rebuild() cmd.refresh() cmd.sort(objSel1) cmd.sort(objSel2) # Provide some useful information stored.allRMSDval = [] stored.allRMSDval = stored.alnAnb + stored.alnBnb print("\nColorByDisplacementAll completed successfully.") print("The MAXIMUM Displacement is: " + str(max(stored.allRMSDval)) + " residue " + str(stored.alnAres[int(stored.allRMSDval.index(max(stored.allRMSDval)))])) if strTrue(doColor): # Showcase what we did # cmd.orient() # cmd.hide("all") cmd.show("sticks", objSel1 + " or " + objSel2) # Select the residues not used for alignment; they still have their B-factors as "-0.2" cmd.select("notUsedForAln", "b = -0.2") # White-wash the residues not used for alignment cmd.color("white", "notUsedForAln") # Select the residues not in both pdb files; they have their B-factors as "-0.01" cmd.select("ResNotInBothPDB", "b = -0.01") # White-wash the residues not used for alignment cmd.color("black", "ResNotInBothPDB") # Color the residues used for alignment according to their B-factors (Displacement values) #cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB") cmd.spectrum("b", 'rainbow', "((" + objSel1 + ") or (" + objSel2 + " )) and not (notUsedForAln or ResNotInBothPDB)") # Delete the selection of atoms not used for alignment # If you would like to keep this selection intact, # just comment "cmd.delete" line and # uncomment the "cmd.disable" line abowe. cmd.disable("notUsedForAln") cmd.delete("notUsedForAln") cmd.disable("ResNotInBothPDB") cmd.delete("ResNotInBothPDB") print("\nObjects are now colored by C-alpha displacement deviation.") print("Blue is minimum and red is maximum...") print("White is those residues used in the alignment algorithm. Can be turned off in top of algorithm.") print("Black is residues that does not exist in both files...") cmd.extend("ColorByDisplacementAll", ColorByDisplacementAll)