Difference between revisions of "Annocryst"

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(Example Pymol Script)
(Example Pymol Script)
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keywordOntologyNamespace: http://www.proteinontology.info/po.owl
 
keywordOntologyNamespace: http://www.proteinontology.info/po.owl
 
keywordOntologyURL: http://maenad.itee.uq.edu.au/agerber/po.owl
 
keywordOntologyURL: http://maenad.itee.uq.edu.au/agerber/po.owl
pdbRepositoryURL:http://maenad.itee.uq.edu.au:8080/harvanapdb/au.edu.uq.itee.eresearch.harvana.gwt.Main/pdb/
+
pdbRepositoryURL: http://maenad.itee.uq.edu.au:8080/harvanapdb/au.edu.uq.itee.eresearch.harvana.gwt.Main/pdb/
 
uploadServerURL: http://maenad.itee.uq.edu.au:8080/Annotea/FileUploadServlet
 
uploadServerURL: http://maenad.itee.uq.edu.au:8080/Annotea/FileUploadServlet
 
username: Anonymous
 
username: Anonymous
 
</syntaxhighlight>
 
</syntaxhighlight>
  
View the settings, and save them.
+
Change following settings, and save them.
 +
pdbRepositoryURL: http://www.rcsb.org/pdb/files/
  
 
Then in the '''PyMOL command window''', write
 
Then in the '''PyMOL command window''', write

Revision as of 21:49, 5 December 2011

AnnoCryst for PyMOL extends the functionality of PyMOL to support collaborative annotation of 3D crystallographic models. It is implemented as a plugin to PyMOL that provides an interface to browse and create annotations on structures loaded from Protein Data Bank (PDB) files. The annotations are retrieved from and stored on an annotation server using the W3C's Annotea protocol.

Website: AnnoyCryst online.

Example Pymol Script

See userguide http://itee.uq.edu.au/~eresearch/downloads/annocryst-pymol-user-guide.pdf

Standard settings of AnnoCryst Settings

annotationsServerURL: http://maenad.itee.uq.edu.au:8080/Annotea/AnnoteaServlet
keywordOntologyNamespace: http://www.proteinontology.info/po.owl
keywordOntologyURL: http://maenad.itee.uq.edu.au/agerber/po.owl
pdbRepositoryURL: http://maenad.itee.uq.edu.au:8080/harvanapdb/au.edu.uq.itee.eresearch.harvana.gwt.Main/pdb/
uploadServerURL: http://maenad.itee.uq.edu.au:8080/Annotea/FileUploadServlet
username: Anonymous

Change following settings, and save them.

pdbRepositoryURL: http://www.rcsb.org/pdb/files/

Then in the PyMOL command window, write

 remotepdb 3ait

In the Annocryst, is now written: http://maenad.itee.uq.edu.au:8080/harvanapdb/au.edu.uq.itee.eresearch.harvana.gwt.Main/pdb/3ait.pdb

Push Open.

Python Code

Download: plugins/annocryst.py
This code has been put under version control in the project Pymol-script-repo