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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|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 | ||
| − | + | This requires that the authors have performed annotation in the pdb file. | |
| − | |||
| − | |||
| − | |||
| − | This requires that the authors | ||
== 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