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Display of TLS fitting of anisotropic B-factors looks like a
difficult problem. Here is a good try at it, a program called
TLSView (part of a package called mmLib), developed by Jay Painter.
Chimera does not do this.<br>
<a class="moz-txt-link-freetext" href="http://pymmlib.sourceforge.net/tlsview/tlsview.html">http://pymmlib.sourceforge.net/tlsview/tlsview.html</a><br>
My understanding is that TLS does a fitting of anisotropic
b-factors for a group of nearby atoms. It is based on the idea that
the motions of these atoms are correlated. It is a quadratic
approximation using position from an arbitrarily chosen origin for
the group of atoms. The fitting is predicting the anisotropic
B-factor for each atom (a tensor with 6 independent components which
determine the 3 principle axes directions and amplitudes along those
directions) and it involves 20 independent parameters. Two very
basic questions given TLS fitting are 1) how much does the TLS fit
differ from the individual atom aniostropic B-factors that produced
the fit? and 2) what coherent motion of the atoms would give rise to
these TLS parameters? A visualization to answer the first question
would be pretty easy, but it requires having both TLS and the
individual atom anisotropic B-factors. The 1SS8 PDB only reports
TLS. The answer for the second question is harder to visualize and
TLSViewer shows 3 orthogonal screw axes that need not go through a
common origin. I get the concept but am not sure how valuable it
is. It would take some examples with specific molecular structures
and specific large scale motions interpreted via TLS for me to
understand this TLSViewer visualization better.<br>
<pre wrap="">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.
<a class="moz-txt-link-rfc2396E" href="http://www.wwpdb.org/docs.html"><http://www.wwpdb.org/docs.html></a>
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:
<a class="moz-txt-link-rfc2396E" href="http://deposit.rcsb.org/adit/REFMAC.html"><http://deposit.rcsb.org/adit/REFMAC.html></a>
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":
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html"><http://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/thermal/thermal.html></a>
<a class="moz-txt-link-rfc2396E" href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/aniso.html"><http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/aniso.html></a>
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
On Apr 24, 2012, at 6:02 AM, Steven Ludtke wrote:
<pre wrap="">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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