Difference between revisions of "Select sites"

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|type      = script
 
|type      = script
 
|filename  = select_sites.py
 
|filename  = select_sites.py
|author    = [[User:Speleo3|Thomas Holder] & [User:Tlinnet|Troels Linnet]]  
+
|author    = [[User:Speleo3|Thomas Holder]] & [[User:Tlinnet|Troels Linnet]]  
 
|license  = BSD-2-Clause
 
|license  = BSD-2-Clause
 
}}
 
}}

Latest revision as of 13:04, 23 July 2012

Type Python Script
Download select_sites.py
Author(s) Thomas Holder & Troels Linnet
License BSD-2-Clause
This code has been put under version control in the project Pymol-script-repo

select_sites make named selections from SITE, LINK, SSBOND, HET records.
A super fast way to annotate the protein, according to the authors input i pdb file.

See:
http://www.wwpdb.org/procedure.html#toc_10

For instance, trypsin (http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES):

SITE     1 CAT  3 HIS A  57  ASP A 102  SER A 195
SITE     1 AC1  6 ASP A 165  ALA A 177A GLU A 180  GLU A 230
SITE     2 AC1  6 HOH A 259  HOH A 261

This requires that the authors have performed annotation in the pdb file.

Usage

import select_sites
select_sites [ selection [, filename [, prefix [, nice [, quiet ]]]]]

nice = 0 or 1: make colored sticks representation for sites {default :1}

Example

fetch 1sgt, async=0
import select_sites
select_sites

Or fetch and select_sites in one go

import select_sites
sites 1sgt

See Also