[Chimera-users] Rendering TLS information in Chimera ?

Elaine Meng meng at cgl.ucsf.edu
Tue Apr 24 10:09:38 PDT 2012

Hi Steve,
While Chimera currently understands PDB ANISOU records and can show that information with thermal ellipsoids, it does not understand TLS information in the header.  I do see the TLS info in the REMARK  3 lines in pdb1ss8.ent, but I didn't see anything in the PDB format specifications.

 However.... at least from these deposition instructions, it sounds like depositors are supposed to convert the TLS information into ANISOU records beforehand.  Also, the page has a server to do the conversion:

Perhaps (at least for now) you could try using the server above, and then Thermal Ellipsoids (in  menu under Tools... Structure Analysis) or command "aniso": 

I did this for 1ss8.  It can be quite busy since it is per-atom, but I tried showing only CA atoms and their ellipsoids for chain A, 90% probability level shown in the image attached below.

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

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On Apr 24, 2012, at 6:02 AM, Steven Ludtke wrote:

> Hi. A question about rendering B-factor information: Over the last decade, rather than simple anisotropic B-factors, it has become increasingly common to represent local "motion" using the translation-libration-screw (TLS) model, which provides for anisotropic representation of such motions. Is there a good way to represent this data in Chimera ?  Here is an example. If you render the PDB structure 1OEL as atoms, and color the atoms by B-factor, you can immediately observe regions of high variability in the apical domain. This same data was later re-refined using a TLS model as PDB structure 1SS8. When you render this structure in Chimera in the same way, you see high B-factors only for a few specific sidechains. The overall large-scale variability is gone, presumably because the TLS parameters have absorbed it, and the "B-factor" is now only a residual B-factor.  However, I can't see any obvious way of rendering the TLS information.  Any tips ?

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