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

Eric Pettersen pett at cgl.ucsf.edu
Thu Dec 11 11:43:17 PST 2008

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 Pettersen
                         UCSF Computer Graphics Lab

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