taskAdun - Tasks: task #6710, integration with Chimera

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task #6710: integration with Chimera

Submitted by:  Jordi VillĂ -Freixa <jvilla>
Submitted on:  Thu Aug 20 19:15:56 2009  
Should Start On: Thu Oct 1 00:00:00 2009Should be Finished on: Sun Jun 20 00:00:00 2010
Category: NonePriority: 1 - Later
Status: NonePrivacy: Public
Percent Complete: 0%Assigned to: None
Open/Closed: OpenPlanned Release: None
Effort: 0.00

Thu Aug 20 19:15:56 2009, original submission:

Stronger integration with Chimera provides an opportunity not just for viaualization of gerenated trajectories and structures, but for a better control of the workflow for Adun simulations. Aspects of this integration include:
1) visualization of Adun trajectories
2) preparations of PDBs prior to the building of the corresponding systems in Adun (side chain completion, hydrogens addition, parameters graphical editing...)
3) steered MD, by controling (almost) at run time trajectories and producing changes in the topology and FF that automatically transfer to Adun to rebuild the system and restart the simulations
4) simple minimizations and relaxations from a chimera extension (check, eg, existing plugins for Dock or AMBER in chimera)
5) others

To start with, the task will include exploring and eventually cloning the way Chimera and Cytoscape are connected through the Cytoscape StructureViz plugin. This is a bidirectional plugin that uses command line tools to access chimera from cytoscape and viceversa.

A second option would be exploring the use of web services, although this can be left for the second generation of the Adun/chimera integration and may be replaced by the builtin distributed computing with Adun (check how Blast is run from chimera)

Jordi VillĂ -Freixa <jvilla>
Project Administrator


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    Follows 1 latest change.

    Date Changed By Updated Field Previous Value => Replaced By
    Mon Dec 21 01:46:18 2015cazfiDependencies-=>task #7924 is dependent
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