Difference between revisions of "Resicolor plugin"

Revision as of 16:31, 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

@@ Line 1: / Line 1: @@
 ==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]]

Difference between revisions of "Resicolor plugin"

Revision as of 16:31, 3 December 2011

Description

Example of use

Python Code

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