Difference between revisions of "Annocryst"

From PyMOLWiki
Jump to: navigation, search
(Python Code)
Line 34: Line 34:

Revision as of 11:11, 15 January 2012

Type PyMOL Plugin
Download plugins/annocryst.py
Author(s) Anna Gerber
License -
This code has been put under version control in the project Pymol-script-repo


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.