Difference between revisions of "Annocryst"

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{{Infobox script-repo
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|type      = plugin
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|filename  = plugins/annocryst.py
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|author    = Anna Gerber
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|license  = -
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}}
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== Introduction ==
 
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.
 
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: [http://www.itee.uq.edu.au/~eresearch/annocryst-pymol.php AnnoyCryst] online.
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Website: [http://www.itee.uq.edu.au/eresearch/projects/annocryst-pymol AnnoyCryst] online.
  
 
== Example Pymol Script ==
 
== Example Pymol Script ==
See userguide http://itee.uq.edu.au/~eresearch/downloads/annocryst-pymol-user-guide.pdf
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See userguide http://www.itee.uq.edu.au/eresearch/downloads/annocryst-pymol-user-guide.pdf
  
 
Standard settings of '''AnnoCryst Settings'''  
 
Standard settings of '''AnnoCryst Settings'''  
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Push Open.
 
Push Open.
 
== Python Code ==
 
 
{{Template:PymolScriptRepoDownload|plugins/annocryst.py}}
 
  
 
[[Category:Plugins]]
 
[[Category:Plugins]]
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[[Category:Pymol-script-repo]]

Latest revision as of 16:56, 30 January 2017

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

Introduction

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://www.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.