This is a read-only mirror of pymolwiki.org

Difference between revisions of "Resicolor plugin"

From PyMOL Wiki
Jump to navigation Jump to search
m (9 revisions)
 
(7 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 +
{{Infobox script-repo
 +
|type      = plugin
 +
|filename  = plugins/resicolor_plugin.py
 +
|author    = [[User:Philaltist|Philaltist]]
 +
|license  = -
 +
}}
 +
 
==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">
 
−
#plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu
 
−
from Tkinter import *
 
−
from pymol import cmd
 
−
import tkSimpleDialog
 
−
 
 
−
def __init__(self):
 
−
    # Simply add the menu entry and callback
 
−
    self.menuBar.addmenuitem('Plugin', 'command',
 
−
                                    'resicolor',
 
−
                                    label = 'resicolor2',
 
−
                                    command = lambda s=self : getselection(s))
 
−
 
 
−
def resicolor(selection):
 
−
    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)
 
−
 
 
−
def getselection(app):
 
−
    selection=tkSimpleDialog.askstring('resicolor',
 
−
                                              'Please enter a selection',
 
−
                                              parent=app.root)
 
−
    resicolor(selection)
 
  
−
</source>
+
== Example of use ==
 +
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.
  
 +
[[Category:Script_Library]]
 +
[[Category:Structural_Biology_Scripts]]
 
[[Category:Plugins]]
 
[[Category:Plugins]]
 +
[[Category:Coloring]]
 +
[[Category:Pymol-script-repo]]

Latest revision as of 03:09, 28 March 2014

Type PyMOL Plugin
Download plugins/resicolor_plugin.py
Author(s) Philaltist
License -
This code has been put under version control in the project Pymol-script-repo

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.

Retrieved from "http://wiki.pymol.org/index.php?title=Resicolor_plugin&oldid=8616"