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Difference between revisions of "Resicolor"

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Hello !
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==Description==
  
Here is a small plugin to color proteins according to residue type. Copy this into a file saved as resicolor.py inside your plugins startup directory, and it should add itself to the plugins menu at the next pymol startup. The script version (accessible from command line) is presented below.
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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.
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This functionality is also available as a plugin ([[Resicolor_plugin]]).
  
<source lang="python">
 
#plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu
 
from Tkinter import *
 
from pymol import cmd
 
 
def __init__(self):
 
    # Simply add the menu entry and callback
 
    self.menuBar.addmenuitem('Plugin', 'command',
 
                                    'resicolor',
 
                                    label = 'resicolor',
 
                                    command = lambda s=self : resicolor(s))
 
class resicolor:
 
    def __init__(self,app):
 
        import tkSimpleDialog
 
        selection=tkSimpleDialog.askstring('resicolor',
 
                                                  'Please enter a selection',
 
                                                  parent=app.root)
 
        if selection:  # None is returned for user cancel
 
            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')   
 
            code={'acid'    :  'red'    ,
 
                  'basic'  :  'blue'  ,
 
                  'nonpolar':  'orange' ,
 
                  'polar'  :  'green'  ,
 
                  'cys'    :  'yellow'}
 
            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
 
</source>
 
 
Here is the corresponding script file. 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.
 
 
<source lang="python">
 
<source lang="python">
 
#script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu
 
#script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu
Line 84: Line 42:
 
cmd.extend ('resicolor',resicolor)
 
cmd.extend ('resicolor',resicolor)
 
</source>
 
</source>
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 +
==Download==
 +
[[Media:Resicolor-0.1.tar.zip‎|Resicolor-0.1.tar.zip‎]]
  
 
[[Category:Script_Library]]
 
[[Category:Script_Library]]
 +
[[Category:Coloring|Resicolor Script]]
 +
[[Category:Biochemical_Scripts]]

Latest revision as of 05:01, 16 November 2015

Description

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. This functionality is also available as a plugin (Resicolor_plugin).

#script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu
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.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)

Download

Resicolor-0.1.tar.zip‎