Resicolor plugin: Difference between revisions

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==Description==
==Description==
Here is a small plugin to color proteins according to residue type. Save the following text as "resicolor.py" in your somewhere/PyMOL/modules/pmg_tk/startup directory, and it should add itself to the plugin menu at the next pymol startup. This functionality is also available as a script ([[resicolor]]).
A small plugin to color proteins according to residue type. This functionality is also available as a script ([[resicolor]]).


<source lang="python">
== Example of use ==
#plugin contributed by Philippe Garteiser garteiserp@omrf.org
If you follow the instructions for the [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo], it is available from the Plugin menu.
from Tkinter import *
from pymol import cmd
import tkSimpleDialog


def __init__(self):
== Python Code ==
    # Simply add the menu entry and callback
This code has been put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo].
    self.menuBar.addmenuitem('Plugin', 'command',
                                    'resicolor',
                                    label = 'resicolor',
                                    command = lambda s=self : getselection(s))


def resicolor(selection):
For a color coded view:
    if selection:   # None is returned for user cancel
https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/resicolor_plugin.py
        cmd.select ('calcium','resn ca or resn cal')
See the raw code or download manually, by right clicking the following link here -> Save as: resicolor_plugin.py
        cmd.select ('acid','resn asp or resn glu or resn cgu')
  https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/plugins/resicolor_plugin.py
        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)


def getselection(app):
[[Category:Script_Library]]
    selection=tkSimpleDialog.askstring('resicolor',
[[Category:Structural_Biology_Scripts]]
                                              'Please enter a selection',
                                              parent=app.root)
    resicolor(selection)
 
</source>


[[Category:Plugins]] [[Category:Coloring]]
[[Category:Plugins]] [[Category:Coloring]]

Revision as of 11:31, 3 December 2011

Description

A small plugin to color proteins according to residue type. This functionality is also available as a script (resicolor).

Example of use

If you follow the instructions for the Pymol-script-repo, it is available from the Plugin menu.

Python Code

This code has been put under version control. In the project, Pymol-script-repo.

For a color coded view: 

https://github.com/Pymol-Scripts/Pymol-script-repo/blob/master/plugins/resicolor_plugin.py

See the raw code or download manually, by right clicking the following link here -> Save as: resicolor_plugin.py 

https://raw.github.com/Pymol-Scripts/Pymol-script-repo/master/plugins/resicolor_plugin.py
Retrieved from "https://pymolwiki.org/index.php?title=Resicolor_plugin&oldid=9900"