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Color by conservation

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
A Random PyMOL-generated Cover. See Covers.