[Chimera-users] size limits on bild geometric primitives?

Scooter Morris scooter at cgl.ucsf.edu
Wed Dec 16 11:24:28 PST 2009

Hi Kristina,
     We also do work in our lab on Cytoscape, which does a lot with 
networks (only 2D, though), so I'd be very interested in your use case 
for your network to see if there are capabilities we should build into 
Cytoscape or Cytoscape and Chimera.


-- scooter

On 12/16/2009 11:15 AM, Thomas Goddard wrote:
> Hi Kristina,
>   If it is just spheres and cylinders you want then you could do it 
> with a Chimera marker model.  You would need your data in an XML 
> format that is explained in the Chimera User's Guide under the Volume 
> Tracer tool:
> http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/volumepathtracer/volumepathtracer.html#markerfiles 
> Marker models act like molecules in Chimera.  You could probably do a 
> similar thing using a PDB file with connect records.
>     Tom
> -------- Original Message --------
> Subject: [Chimera-users] size limits on bild geometric primitives?
> From: Kristina Furse
> To: chimera-users
> Date: 12/16/09 9:29 AM
>> Hi-
>> I like to use Chimera as a front end to povray to make high 
>> resolution images of molecules. I'm starting to work with other types 
>> of data, and was wondering if I could still use it. I have some 
>> network data--20,000 nodes with 32,000 connections. I translated the 
>> data into drawing instructions in bild format--spheres for the nodes 
>> and cylinders for the connections. Small test data sets work (300 
>> nodes with 500 connections or 20,000 spheres with vectors instead of 
>> cylinders) but the full data set of spheres and cylinders crashes 
>> Chimera.
>> Is there a limit somewhere I could raise or is this a hard wall for 
>> bild shapes? Would it be less memory intensive to create a "pdb" of 
>> the node locations and create the connections as bonds?
>> Thanks!
>> Kristina
>> Kristina Furse Davis, Ph.D.
>> Visualization Scientist
>> Center for Research Computing
>> University of Notre Dame
>> P.O. Box 539
>> Room 122 Information Technology Center
>> Notre Dame, IN 46556
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