size limits on bild geometric primitives?
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 kristina.davis@nd.edu
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/vo... 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
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. Thanks! -- 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/vo...
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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I went the pdb with connect records route--works great. Good to know about the marker models. Thank you very much! Kristina On Dec 16, 2009, at 2:15 PM, 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/vo...
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
participants (3)
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Kristina Furse -
Scooter Morris -
Thomas Goddard