Resicolor plugin - Revision history

Bell: 9 revisions

2014-03-28T03:09:00Z

9 revisions

Tlinnet at 15:14, 15 January 2012

2012-01-15T15:14:42Z

Tlinnet at 22:12, 11 December 2011

2011-12-11T22:12:58Z

Tlinnet: /* Python Code */

2011-12-04T15:10:15Z

Python Code

Tlinnet: /* Description */

2011-12-03T16:31:59Z

Description

New page

==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 [http://www.pymolwiki.org/index.php/Git_intro Pymol-script-repo], it is available from the Plugin menu.

== Python Code ==
This code has been put under version control. In the project, [http://www.pymolwiki.org/index.php/Git_intro 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

[[Category:Script_Library]]
[[Category:Structural_Biology_Scripts]]

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

Philaltist at 01:53, 30 July 2008

2008-07-30T01:53:27Z

Philaltist at 18:53, 21 April 2007

2007-04-21T18:53:31Z

Philaltist at 18:39, 21 April 2007

2007-04-21T18:39:26Z

Philaltist: New page: ==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 ...

2007-04-21T18:36:08Z

New page: ==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 ...

New page

==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.

<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>

[[Category:Plugins]]

← Older revision		Revision as of 15:14, 15 January 2012
Line 16:		Line 16:
	[[Category:Plugins]]		[[Category:Plugins]]
	[[Category:Coloring]]		[[Category:Coloring]]
		+	[[Category:Pymol-script-repo]]

← Older revision	Revision as of 03:09, 28 March 2014
(No difference)

@@ Line 1: / Line 1: @@
 ==Description==
 A small plugin to color proteins according to residue type. This functionality is also available as a script ([[resicolor]]).
@@ Line 4: / Line 11: @@
 == 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]]

@@ Line 6: / Line 6: @@
 == Python Code ==
-For a color coded view:
+{{Template:PymolScriptRepoDownload|plugins/resicolor_plugin.py}}
 [[Category:Script_Library]]
 [[Category:Structural_Biology_Scripts]]
 [[Category:Plugins]]
-[[Category:Plugins]] [[Category:Coloring]]
+[[Category:Coloring]]

@@ Line 3: / Line 3: @@
 <source lang="python">
-#plugin contributed by Philippe Garteiser garteiserp@omrf.ouhsc.edu
+#plugin contributed by Philippe Garteiser garteiserp@omrf.org
 from Tkinter import *
 from pymol import cmd

@@ Line 12: / Line 12: @@
      self.menuBar.addmenuitem('Plugin', 'command',
                                       'resicolor',
-                                      label = 'resicolor2',
+                                      label = 'resicolor',
                                       command = lambda s=self : getselection(s))