[Chimera-users] (Thermal ellipsoids) anisotropic temperature factor ellipsoids

Tom Goddard goddard at cgl.ucsf.edu
Fri Dec 12 09:58:08 PST 2008

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).


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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