Difference between revisions of "ColorByDisplacement"

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== Acknowledgement ==
+
#REDIRECT [[colorbydisplacement]]
−
This script is based on the scaffold from [[ColorByRMSD]]. Peace love and harmomy goes to Shivender Shandilya and Jason Vertrees.
 
−
 
 
−
== Introduction ==
 
−
This script allows you to color two structures by distance displacement between an Open and Closed form of a protein, as calculated by PyMol's internal distance command. The pairwise distance is calculated between, C-alpha or all-atoms. The distance displacement values are stored as B-factors of these residues, which are colored by a ''rainbow'' color spectrum, with blue specifying minimum  and red indicating maximum.
 
−
 
 
−
== Code ==
 
−
Do keep in mind, all original B-factors values are overwritten!
 
−
 
 
−
There exist two versions. <br>
 
−
ColorByDisplacement'''CA''' is quick and is between CA atoms. Ideal for helices representation. <br>
 
−
ColorByDisplacement'''All''' is between All atoms in residues and is quite slow => 3-5 mins for a run. Ideal for sticks representation.
 
−
 
 
−
'''You have to specify which residues should be used in the alignment procedure, or it will take all residues as standard'''
 
−
 
 
−
V.2 is implemented the 2011.01.06 - Due to a bug in coloring.
 
−
 
 
−
== Bug in code ==
 
−
A bug in the boolean operator of the spectrum command has been found. This versions work for version 1.3 Educational product. <br>
 
−
For other versions of pymol, try to change (comment/uncomment) the '''cmd.spectrum''' line.
 
−
The other spectrum line works for Open-Source PyMOL 1.2r3pre, Incentive product
 
−
 
 
−
=== Examples ===
 
−
<source lang="python">
 
−
ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
−
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
−
 
 
−
ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'
 
−
ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t, AlignedWhite='no'
 
−
 
 
−
ColorByDisplacementCA O5NT, C5NT, resi 26-355, resi 26-355
 
−
ColorByDisplacementAll O5NT, C5NT, resi 26-355, resi 26-355
 
−
</source>
 
−
 
 
−
<gallery heights="240px" widths="340px">
 
−
Image:ColorByDisplacement-CA-1.png|ColorByDisplacementCA used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
−
Image:ColorByDisplacement-CA-2.png|ColorByDisplacementCA used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
−
Image:ColorByDisplacement-All-1.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
−
Image:ColorByDisplacement-All-2.png|ColorByDisplacementAll used on 1HP1 and 1HPU aligned and colored by distance displacement.
 
−
</gallery>
 
−
Dark blue is low displacement, higher displacements are in orange/yellow/red. <br>
 
−
Residues used for alignment is colored white. Can be turned off in top of algorithm.
 
−
Residues not in both pdb files is colored black
 
−
 
 
−
== Example Pymol Script ==
 
−
<source lang="python">
 
−
cd C:\Users\tlinnet\Documents\My Dropbox\Speciale\5NT-project\Mutant-construct\Distance-Plot
 
−
#cd /homes/linnet/Documents/Speciale/5NT-project/Mutant-construct/Distance-Plot
 
−
### load pdb files and rename
 
−
load 1HP1.pdb, O5NT-1HP1
 
−
load 1HPU.pdb, C5NT-1HPU
 
−
 
 
−
hide everything
 
−
### Select asymmetric units from pdb file
 
−
create O5NT, /O5NT-1HP1//A
 
−
create C5NT, /C5NT-1HPU//C
 
−
delete O5NT-1HP1
 
−
delete C5NT-1HPU
 
−
 
 
−
cartoon auto
 
−
show cartoon, O5NT
 
−
show cartoon, C5NT
 
−
set cartoon_fancy_helices=1
 
−
set bg,[1,1,1]
 
−
 
 
−
set auto_zoom, off
 
−
 
 
−
### Make sharper
 
−
set fog=0
 
−
 
 
−
### Load my function, and run function with input
 
−
run ColorByDisplacement.py
 
−
ColorByDisplacementCA O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
−
#ColorByDisplacementAll O5NT, C5NT, super1=resi 26-355, super2=resi 26-355, doColor=t, doAlign=t
 
−
 
 
−
set_view (\
 
−
    0.094686687,  -0.390707940,    0.915631354,\
 
−
    0.809000611,  -0.505792081,  -0.299485058,\
 
−
    0.580131471,    0.769104064,    0.268191338,\
 
−
    0.000000000,    0.000000000, -280.940521240,\
 
−
    26.240486145,  46.146961212,  21.702068329,\
 
−
  231.830673218,  330.050415039,  -20.000000000 )
 
−
</source>
 
−
 
 
−
 
 
−
== Python Code ==
 
−
<source lang="python">
 
−
import pymol
 
−
import cmd
 
−
from pymol import stored
 
−
 
 
−
### Thanks for inspiration from:
 
−
"""
 
−
--- ColorByRMSD: RMSD based coloring ---
 
−
Authors : Shivender Shandilya; Jason Vertrees
 
−
Program : ColorByRMSD
 
−
Date    : July 2009
 
−
http://www.pymolwiki.org/index.php/ColorByRMSD
 
−
"""
 
−
### Author Troels Linnet - troels.linnet att bbz.uni-leipzig.de
 
−
"""
 
−
--- ColorByDisplacementCA: Displacement based coloring ---
 
−
Authors : Troels E. Linnet
 
−
Program : ColorByDisplacementCA
 
−
Date    : January 2011
 
−
email: troels.linnet att bbz.uni-leipzig.de
 
−
"""
 
−
 
 
−
"""
 
−
    ColorByDisplacementCA --
 
−
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.
 
−
 
 
−
"""
 
−
 
 
−
def strTrue(p):
 
−
    return p[0].upper() == "T"
 
−
 
 
−
# The main function that assigns current displacement distance as the new B-factor
 
−
def displacementUpdateB(objA, alnAri, objB, alnBri):
 
−
    ### If residue is unassigned in one of the pdb files, we reset its value
 
−
    for x in range(len(alnAri)):
 
−
        s1 = objA + " and name CA and resi " + alnAri[x]
 
−
cmd.alter( s1, "b = " + str(-0.01))
 
−
    for x in range(len(alnBri)):
 
−
s2 = objB + " and name CA and resi " + alnBri[x]
 
−
        cmd.alter( s2, "b = " + str(-0.01))
 
−
    cmd.sort(objA); cmd.sort(objB)
 
−
    for x in range(len(alnAri)):
 
−
        s1 = objA + " and name CA and resi " + alnAri[x]
 
−
s2 = objB + " and name CA and resi " + alnAri[x]
 
−
### 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 ColorByDisplacementCA(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
 
−
    if AlignedWhite=='yes':
 
−
        cmd.iterate(tObj1 + " and n. CA and not " + aln, "stored.alnAres.append(resi)")
 
−
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBres.append(resi)")
 
−
    else:
 
−
cmd.iterate(tObj1 + " and n. CA", "stored.alnAres.append(resi)")
 
−
        cmd.iterate(tObj2 + " and n. CA", "stored.alnBres.append(resi)")
 
−
 
 
−
    ### Change the B-factors for EACH object
 
−
    displacementUpdateB(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 n. CA and not " + aln, "stored.alnAnb.append(b)" )
 
−
cmd.iterate(tObj2 + " and n. CA and not " + aln, "stored.alnBnb.append(b)" )
 
−
    else:
 
−
### Or Iterate over all objects with CA
 
−
    cmd.iterate(tObj1 + " and n. CA", "stored.alnAnb.append(b)" )
 
−
    cmd.iterate(tObj2 + " and n. CA", "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
 
−
    for x in range(len(stored.alnAres)):
 
−
        cmd.alter(objSel1 + " and n. CA and i. " + str(stored.alnAres[x]), "b = " + str(stored.alnAnb[x]))
 
−
    for x in range(len(stored.alnBres)):
 
−
        cmd.alter(objSel2 + " and n. CA and i. " + str(stored.alnBres[x]), "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 "\nColorByDisplacementCA 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("cartoon", 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 (Displacment values)
 
−
#        cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + objSel2 +" )) and not notUsedForAln+ResNotInBothPDB")
 
−
        cmd.spectrum("b", 'rainbow',  "((" + objSel1 + " and n. CA) or (n. CA and " + 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("ColorByDisplacementCA", ColorByDisplacementCA)
 
−
 
 
−
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)
 
−
</source>
 
−
 
 
−
[[Category:Script_Library]]
 
−
[[Category:Structural_Biology_Scripts]]
 

Latest revision as of 10:08, 1 December 2011

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