Resicolor

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Revision as of 10:15, 10 April 2007 by Philaltist (talk | contribs) (New page: Hello ! Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: "run resicolor.py". Then, issuing "resicolor" will apply the s...)
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Hello !

Here is a small script to color proteins according to residue type. Call it from your .pymolrc or from within pymol: "run resicolor.py". Then, issuing "resicolor" will apply the scheme. Selections are supported: "resicolor chain A" will apply the scheme only to chain A.

from pymol import cmd

def resicolor(selection='all'):

   USAGE: resicolor <selection>
   colors all or the given selection with arbitrary
   coloring scheme.
   
   cmd.select ('calcium','resn ca or resn cal')
   cmd.select ('acid','resn asp or resn glu or resn cgu')
   cmd.select ('basic','resn arg or resn lys or resn his')
   cmd.select ('nonpolar','resn met or resn phe or resn pro or resn trp or resn val or resn leu or resn ile or resn ala')
   cmd.select ('polar','resn ser or resn thr or resn asn or resn gln or resn tyr')
   cmd.select ('cys','resn cys or resn cyx')
   cmd.select ('backbone','name ca or name n or name c or name o')
   cmd.select ('none')
   print selection
   code={'acid'    :  'red'    ,
         'basic'   :  'blue'   ,
         'nonpolar':  'orange' ,
         'polar'   :  'green'  ,
         'cys'     :  'yellow'}
   cmd.do ('getchem')
   cmd.select ('none')
   for elem in code:
       line='color '+code[elem]+','+elem+'&'+selection
       print line
       cmd.do (line)
   word='color white,backbone &'+selection
   print word
   cmd.do (word)                  #Used to be in code, but looks like
                                  #dictionnaries are accessed at random
   cmd.hide ('everything','resn HOH')

cmd.extend ('resicolor',resicolor)