[Chimera-users] Trouble with thermal ellipsoids

Elaine Meng meng at cgl.ucsf.edu
Tue Mar 30 10:00:17 PDT 2010

Hi Nat,
You are not doing anything wrong -- it may be that you need a newer  
version of Chimera.

For a while Chimera only read the anisotropic B-factor information  
from PDB files.  I believe that is true for version 1.4, but if you  
get version 1.5 (in the daily builds part of the download page) it  
should work with CIF anisotropy information too.  I just tried a CIF  
file of my own with both these versions.  Guess this should be  
mentioned in the "what's new" release notes, but I didn't know until  
now that the problem had been fixed!

I hope this helps,
Elaine C. Meng, Ph.D.
UCSF Computer Graphics Lab (Chimera team) and Babbitt Lab
Department of Pharmaceutical Chemistry
University of California, San Francisco

On Mar 30, 2010, at 1:19 AM, sherden at caltech.edu wrote:

> I can't seem to get the thermal ellipsoids to work.  I have a number  
> of
> .cif files that are all perfectly good files (have been cif-checked)  
> and
> all of which I know for a fact have anisotropic data as I can get  
> thermal
> ellipsoids to display from these files in other programs like Diamond
> (which we are trying to move away from).  But any time I select an  
> atom or
> group of atoms and use either the "aniso" command or the "Show Thermal
> Ellipsoids" dialogue box I just get: "No atoms chosen had anisotropic
> information."  This is just not true though, I can open up the .cif  
> files
> in question and see the anisotropic data listed for the given atoms  
> with
> my own two eyes.
>  Any thoughts?  I am probably doing something immensely stupid, that  
> is
> usually the case with such situations.
>   --Nat (Nathaniel Sherden)
> California Institute of Technology
> Department of Chemistry

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