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| + | {{Infobox script-repo | ||
| + | |type = plugin | ||
| + | |filename = plugins/annocryst.py | ||
| + | |author = Anna Gerber | ||
| + | |license = - | ||
| + | }} | ||
| + | |||
| + | == 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/ | + | 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/ | + | 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''' | ||
| Line 11: | Line 19: | ||
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> | ||
| − | + | 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 | ||
| Line 22: | Line 31: | ||
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 | ||
| − | + | Push Open. | |
| − | |||
| − | |||
[[Category:Plugins]] | [[Category:Plugins]] | ||
| + | [[Category:Pymol-script-repo]] | ||
Latest revision as of 03:04, 6 February 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.