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Difference between revisions of "Color by conservation"

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|type      = script
 
|type      = script
 
|filename  = color_by_conservation.py
 
|filename  = color_by_conservation.py
|author    = [[Users:Inchoate|Jason Vertrees]]
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|author    = [[User:Inchoate|Jason Vertrees]]
 
|license  = Free
 
|license  = Free
 
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[[Category:Script_Library]]
 
[[Category:Script_Library]]
 
[[Category:Structural_Biology_Scripts]]
 
[[Category:Structural_Biology_Scripts]]
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[[Category:Pymol-script-repo]]

Latest revision as of 01:43, 28 March 2014

Type Python Script
Download color_by_conservation.py
Author(s) Jason Vertrees
License Free
This code has been put under version control in the project Pymol-script-repo

Overview

This script reads an alignment object and colors the protein objects in the alignment by the sequence conservation found in the alignment.

Cbcon.png

Example Usage

reinitialize
import color_by_conservation
 
# get some kinases
fetch 1opk 3dtc 3p86 2eva 3efw, async=0
 
# turn on the sequence viewer
set seq_view

# align them into the "algn" object
for x in cmd.get_names(): cmd.align(x, "3efw and c. A", object="algn")
 
# color
color_by_conservation aln=algn, as_putty=1