[Chimera-users] Rendering TLS information in Chimera ?

Steven Ludtke sludtke at bcm.edu
Tue Apr 24 06:02:06 PDT 2012

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 ?

Steven Ludtke, Ph.D.
Associate Professor
Co-Director National Center For Macromolecular Imaging        (ncmi.bcm.edu)
Co-Director CIBR Center                          (www.bcm.edu/research/cibr)
Dept of Biochemistry and Mol. Biol.                    (www.bcm.edu/biochem)
Baylor College of Medicine                              
sludtke at bcm.edu
stevel at alumni.caltech.edu

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