[Chimera-users] Rendering TLS information in Chimera ?

[Elaine Meng]

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.
<http://www.wwpdb.org/docs.html>

 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:
<http://deposit.rcsb.org/adit/REFMAC.html>

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": 
<http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html>
<http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/aniso.html>

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

-------------- next part --------------
A non-text attachment was scrubbed...
Name: image.png
Type: image/png
Size: 159507 bytes
Desc: not available
URL: <http://plato.cgl.ucsf.edu/pipermail/chimera-users/attachments/20120424/49b6b529/attachment.png>
-------------- next part --------------

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 ?
>