Resicolor - Revision history

Bell: 1 revision

2015-11-16T05:01:10Z

1 revision

Bell at 17:32, 31 October 2015

2015-10-31T17:32:06Z

Bell at 17:30, 31 October 2015

2015-10-31T17:30:31Z

Bell: 11 revisions

2014-03-28T03:49:14Z

11 revisions

New page

==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]]).

<source lang="python">
#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)
</source>

==Download==
[[Media:Resicolor-0.1.tar.bz2‎|Resicolor-0.1.tar.bz2‎]]

[[Category:Script_Library]]
[[Category:Coloring|Resicolor Script]]
[[Category:Biochemical_Scripts]]

Desastre at 17:47, 12 January 2008

2008-01-12T17:47:41Z

New page

Philaltist at 18:41, 21 April 2007

2007-04-21T18:41:11Z

Philaltist at 18:37, 21 April 2007

2007-04-21T18:37:54Z

Philaltist at 18:27, 21 April 2007

2007-04-21T18:27:17Z

Philaltist at 20:25, 10 April 2007

2007-04-10T20:25:05Z

Philaltist at 19:01, 10 April 2007

2007-04-10T19:01:43Z

@@ Line 2: / Line 2: @@
 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.
+This functionality is also available as a [http://pymolwiki.org/index.php/Resicolor_plugin plugin].
 <source lang="python">

@@ Line 4: / Line 4: @@
 <source lang="python">
 from Tkinter import *
 from pymol import cmd
@@ Line 19: / Line 20: @@
                                                    'Please enter a selection',
                                                    parent=app.root)
-         if 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')
@@ Line 47: / Line 48: @@
 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">
 from pymol import cmd

← Older revision	Revision as of 05:01, 16 November 2015
(No difference)

← Older revision	Revision as of 17:32, 31 October 2015
(No difference)

@@ Line 44: / Line 44: @@
 ==Download==
-[[Media:Resicolor-0.1.tar.bz2‎|Resicolor-0.1.tar.bz2‎]]
+[[Media:Resicolor-0.1.tar.zip‎|Resicolor-0.1.tar.zip‎]]
 [[Category:Script_Library]]
 [[Category:Coloring|Resicolor Script]]
 [[Category:Biochemical_Scripts]]

@@ Line 1: / Line 1: @@
 Hello !
-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.
+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.
 <source lang="python">
 #script contributed by Philippe Garteiser; garteiserp@omrf.ouhsc.edu

@@ Line 34: / Line 34: @@
                    'polar'   :  'green'  ,
                    'cys'     :  'yellow'}
              cmd.select ('none')
              for elem in code:
@@ Line 72: / Line 71: @@
            'polar'   :  'green'  ,
            'cys'     :  'yellow'}
      cmd.select ('none')
      for elem in code: