@@ Line 1: / Line 1: @@
-== 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 a 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>
-ColorByDisplacementCA is quick and is between CA atoms. Ideal for helices representation. <br>
-ColorByDisplacementAll 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.
-=== 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, 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 (\
-.094686687,   -0.390707940,    0.915631354,\
-.809000611,   -0.505792081,   -0.299485058,\
-.580131471,    0.769104064,    0.268191338,\
-.000000000,    0.000000000, -280.940521240,\
-.240486145,   46.146961212,   21.702068329,\
-.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]]

Difference between revisions of "ColorByDisplacement"

Latest revision as of 02:15, 28 March 2014

Navigation menu

Search