Difference between revisions of "Select sites"

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(Created page with "{{Infobox script-repo |type = script |filename = select_sites.py |author = Thomas Holder |license = BSD-2-Clause }} select_sites make named sele...")
 
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[[select_sites]] make named selections from SITE records.
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[[select_sites]] make named selections from SITE 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
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SITE    1 AC1  6 ASP A 165  ALA A 177A GLU A 180  GLU A 230
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SITE    2 AC1  6 HOH A 259  HOH A 261
  
SITE    1 CAT  3 HIS A  57  ASP A 102  SER A 195
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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 ==
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  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}
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 +
== Example ==
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<syntaxhighlight lang="python">
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fetch 1sgt, async=0
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import select_sites
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select_sites
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</syntaxhighlight>
  
 
== See Also ==
 
== See Also ==

Revision as of 09:43, 14 July 2012

Type Python Script
Download select_sites.py
Author(s) Thomas Holder
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 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

See Also