[phenixbb] Questions on TLS output and more info on phenix.tls

Michael Garavito garavito at msu.edu
Mon May 29 17:58:11 PDT 2017

I am finishing the final stages of refinement with TLS at 1.7 Å and want to begin some B-factor analysis.  Also, I am setting up for a series of ensemble refinements. However, I am second guessing myself and have been finding that several basic questions that are not explicitly answered by the Phenix documentation.

(1) Just to be sure, I looked for the definition of what is written in the ATOM records of the output PDB file after refinement with TLS:  residual B or total B (residual B + TLS contribution). I always thought the latter after refinement with TLS, but nothing was explicitly stated.

(2) Also, I have looked for it extensively in the Phenix documentation, I have not found any information on phenix.tls, even though in several places (e.g., phenix.ensemble_refinement), there are explicit references to phenix.tls:  “If TLS is used the TLS components must be present in the atom records (see phenix.tls)”  The information from just doing % phenix.tls -h does not give enough insight into options and there use.

Can someone point me to the right place to get these answers?



R. Michael Garavito, Ph.D.
Professor of Biochemistry & Molecular Biology
513 Biochemistry Bldg.   
Michigan State University      
East Lansing, MI 48824-1319
Office:  (517) 355-9724     Lab:  (517) 353-9125
FAX:  (517) 353-9334        Email:  garavito at msu.edu

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20170529/a8c3de88/attachment.htm>

More information about the phenixbb mailing list