Select sites: Difference between revisions
Jump to navigation
Jump to 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...") |
No edit summary |
||
| (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 | |||
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 12:04, 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