(Thermal ellipsoids) anisotropic temperature factor ellipsoids
Dear Chimera team, It looks like preserving PDB ANISOU in Chimera is now a solved problem and I was just wondering if the ability to display anisotropic temperature factor ellipsoids would be added soon. Our small molecule lab and molecular observatory at Caltech is starting to use Chimera and I think small molecule crystallography labs in general would use Chimera more if this feature were available. I do have to admit that I am interested in this feature for selfish reasons. I am using Chimera for several publications and for the graphics in my thesis which, has to be finished in the next couple of weeks, and I would really like to use this feature. Thanks in advance, Dave Chenoweth ********************************************** David M. Chenoweth California Institute of Technology Division of Chemistry and Chemical Engineering Mail Code: 164-30 1200 California Boulevard, 91125 Pasadena California, USA Phone: 626-395-6074 Email: dchen@caltech.edu **********************************************
On Dec 10, 2008, at 3:41 PM, David Chenoweth wrote:
Dear Chimera team,
It looks like preserving PDB ANISOU in Chimera is now a solved problem and I was just wondering if the ability to display anisotropic temperature factor ellipsoids would be added soon. Our small molecule lab and molecular observatory at Caltech is starting to use Chimera and I think small molecule crystallography labs in general would use Chimera more if this feature were available. I do have to admit that I am interested in this feature for selfish reasons. I am using Chimera for several publications and for the graphics in my thesis which, has to be finished in the next couple of weeks, and I would really like to use this feature.
Hi Dave, Yes, reading/preserving the ANISOU info lays the groundwork for eventually showing anisotropic ellipsoids. There's still a lot of work to go before showing the ellipsoids becomes a usable feature of Chimera. It might make it into our next release (middle of next year) and it might not. As a stopgap, I've attached a script that will show ellipsoids for any currently selected atoms. You can run it by simply using File->Open or the "open" command. The first two lines of the script control the size and color of the ellipsoids, so change them if you like. The script leverages some code that Tom Goddard wrote for showing principal axes of inertia as an ellipsoid. Good luck with the thesis! --Eric Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
The script for drawing aniosotropic b-factor ellipsoids makes uses 1280 triangles per ellipsoid surface which slows down your graphics for cases with more than 1000 ellipsoids. You can reduce the "subdivision_levels = 3" in the script to "subdivision_levels = 1" to use just 80 triangles, or to a value of 2 for 320 triangles. The number of triangles controls how smooth the ellipsoid looks (T = 20 * 4^S, S = subdivision_levels). Tom Eric Pettersen wrote:
On Dec 10, 2008, at 3:41 PM, David Chenoweth wrote:
Dear Chimera team,
It looks like preserving PDB ANISOU in Chimera is now a solved problem and I was just wondering if the ability to display anisotropic temperature factor ellipsoids would be added soon. Our small molecule lab and molecular observatory at Caltech is starting to use Chimera and I think small molecule crystallography labs in general would use Chimera more if this feature were available. I do have to admit that I am interested in this feature for selfish reasons. I am using Chimera for several publications and for the graphics in my thesis which, has to be finished in the next couple of weeks, and I would really like to use this feature.
Hi Dave, Yes, reading/preserving the ANISOU info lays the groundwork for eventually showing anisotropic ellipsoids. There's still a lot of work to go before showing the ellipsoids becomes a usable feature of Chimera. It might make it into our next release (middle of next year) and it might not. As a stopgap, I've attached a script that will show ellipsoids for any currently selected atoms. You can run it by simply using File->Open or the "open" command. The first two lines of the script control the size and color of the ellipsoids, so change them if you like. The script leverages some code that Tom Goddard wrote for showing principal axes of inertia as an ellipsoid. Good luck with the thesis!
--Eric
Eric Pettersen UCSF Computer Graphics Lab http://www.cgl.ucsf.edu
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participants (3)
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David Chenoweth -
Eric Pettersen -
Tom Goddard