Difference between revisions of "Annocryst"

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(Example Pymol Script)
(Example Pymol Script)
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   remotepdb 3ait
 
   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
 
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
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Push Open.
  
 
== Python Code ==
 
== Python Code ==

Revision as of 21:38, 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

View the settings, and save them.

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