Difference between revisions of "Select sites"

From PyMOLWiki
Jump to: navigation, search
(Created page with "{{Infobox script-repo |type = script |filename = select_sites.py |author = Thomas Holder |license = BSD-2-Clause }} select_sites make named sele...")
 
 
(4 intermediate revisions by the same user not shown)
Line 2: Line 2:
 
|type      = script
 
|type      = script
 
|filename  = select_sites.py
 
|filename  = select_sites.py
|author    = [[User:Speleo3|Thomas Holder]]  
+
|author    = [[User:Speleo3|Thomas Holder]] & [[User:Tlinnet|Troels Linnet]]  
 
|license  = BSD-2-Clause
 
|license  = BSD-2-Clause
 
}}
 
}}
  
[[select_sites]] make named selections from SITE records.
+
[[select_sites]] make named selections from SITE, LINK, SSBOND, HET records.<br>
 +
A super fast way to annotate the protein, according to the authors input i pdb file.
  
 +
See: <br>
 
http://www.wwpdb.org/procedure.html#toc_10
 
http://www.wwpdb.org/procedure.html#toc_10
  
 
For instance, trypsin (http://www.rcsb.org/pdb/files/1SGT.pdb?headerOnly=YES):
 
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
  
SITE    1 CAT  3 HIS A  57  ASP A 102  SER A 195
+
This requires that the authors have performed annotation in the pdb file.
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 actually perform the annotation.
 
  
 
== Usage ==
 
== Usage ==
Line 22: Line 23:
 
  select_sites [ selection [, filename [, prefix [, nice [, quiet ]]]]]
 
  select_sites [ selection [, filename [, prefix [, nice [, quiet ]]]]]
 
nice = 0 or 1: make colored sticks representation for sites {default :1}
 
nice = 0 or 1: make colored sticks representation for sites {default :1}
 +
 +
== Example ==
 +
<syntaxhighlight lang="python">
 +
fetch 1sgt, async=0
 +
import select_sites
 +
select_sites
 +
</syntaxhighlight>
 +
 +
Or fetch and select_sites in one go
 +
<syntaxhighlight lang="python">
 +
import select_sites
 +
sites 1sgt
 +
</syntaxhighlight>
  
 
== See Also ==
 
== See Also ==

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