AAindex

Hydrophobicity coloring with KYTJ820101

AAindex is a database of numerical indices representing various physicochemical and biochemical properties of amino acids and pairs of amino acids. See http://www.genome.jp/aaindex/

This script is a python parser for the AAindex flat files which will be downloaded from ftp://ftp.genome.jp/pub/db/community/aaindex/

The script provides two PyMOL commands (but can also be used without PyMOL).

• aaindex2b: Loads numerical indices from aaindex1 as b-factors into your structure
• pmf: Potential of Mean Force (aaindex3)

Python Example

Consider the script is called aaindex.py, it is placed somewhere in your PYTHONPATH and the aaindex flatfiles are found in the current directory.

import aaindex
aaindex.init(path='.')

aaindex.grep('volume')
x = aaindex.get('KRIW790103')
print x
print x.get('A')

aaindex.grep('blosum')
x = aaindex.get('HENS920102')
print x.get('A', 'K')

PyMOL Example

import aaindex
aaindex2b KYTJ820101
spectrum b, yellow_white_blue
show surface

Python Code

Download: aaindex.py

This code has been put under version control in the project Pymol-script-repo

See Also

• Protscale from rTools does a similar job in coloring by amino acid properties