[phenixbb] PDBTools and TLS

Mark Saper saper at umich.edu
Thu Aug 29 14:32:46 PDT 2013


I couldn't find the answers to these questions in the documentation.

1. If I am refining TLS and individual isotropic ADPs, does phenix.refine derive iso-ADP from the ANISOU records presently in the file, or does it use the iso-ADP from the ATOM record and recombine it with the TLS values?  

2. Consequently if I reset the B's for a range of residues on the ATOM cards only, will they be used rather than the ANISOU record to derive the ADP?  Is it better to use PDBTools, specify the iso-ADP and also convert to ANISOU?  I am doing this for only a selection of the residues.  

3. Should phenix.refine input files retain the header lines containing the previously cycle TLS parameters?  If so PDB Tools doesn't save them.  PDB Editor does. Which is the preferred tool?

4. If one explicitly changes atom ADPs with Coot using Measures>Residue info...  the output file reflects the change only in the ATOM lines, but the ANISOU line retains the previous 6 parameters.  It seems as if coot should also change the ANISOU to reflect anisou (last 3 parameters=0).

Comments or answers?

Many thanks in advance!

Mark A. Saper, Ph.D.
Department of Biological Chemistry, University of Michigan Medical School
3040 Chemistry Building  |  saper at umich.edu  |  +1 (734) 764-3353  

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