[phenixbb] refmac,tlsanl vs TLS, B and anisou

Paul Adams PDAdams at lbl.gov
Sat Mar 29 18:26:30 PDT 2008

Some comments:

- We (the PHENIX developers) are working with the PDB to come up with  
a more
   streamlined deposition of TLS information for PHENIX. There are  
some other
   issues that need to be resolved first that have slowed this down a  
- I am in agreement with George (not unusual).
- As far as I remember Garib was supportive of the idea of no longer  
   residual B-factors in the atomic iso-B column.
- What phenix.refine writes in the PDB file is almost exactly the  
same as you
   would get by running TLSANL on a REFMAC PDB file.
- It is my understanding that the EBI runs TLSANL on REFMAC deposited  
PDB files
   to extract the ANISOU records so that R-factors can be calculated.  
It would
   seems that this information is then discarded. [I could be  
mistaken about this
   whole process though]
- Allowing ANISOU records only when atomic anisotropic displacement  
   have been refined seems very restrictive. There may be multiple  
ways to arrive
   at anisotropic displacements other than the traditional method  
(TLS is one,
   George mentioned TLS restraints instead of constraints, and we  
have some ideas
   about ADP refinement that would also result in anisotropic  
- It is good to remember that TLS refinement is constrained anisotropic
   displacement parameter refinement.
- If we want bioinformaticians to analyze our structures then we  
should be
   writing something in the iso-B column that they can understand - I  
favour the
   iso-B equivalent of the total atomic B-factor. This I assume they can
   handle. I very much doubt that anyone other than a  
crystallographer will go
   to the trouble of extracting the TLS information and recalculating  
- The biologists looking at structures from the PDB do not care about  
TLS or
   ANISOU records. If they choose to look at anything it will be the  
   column (probably by colouring the atoms by B-factor in a display  
   I'd like to give them a fighting chance of seeing something  
meaningful such
   as the iso-B equivalent of the total atomic B-factor rather than a  
   B-factor (which has no meaning to them).
- I will not be holding my breath waiting for any of the popular  
display programs
   to start interpreting TLS header information.
- I agree that it is best for everyone if we have some clear  
standards for
   deposition and tags that make it clear to anyone looking at files  
from the
   PDB what is meant by the contents. The PDB is very aware of this  
and I expect
   things to be straightened out fairly soon in collaboration with  
the developers
   of phenix.refine and REFMAC.

Paul Adams
Deputy Division Director, Physical Biosciences Division, Lawrence  
Berkeley Lab
Adjunct Professor, Department of Bioengineering, U.C. Berkeley
Vice President for Technology, the Joint BioEnergy Institute
Head, Berkeley Center for Structural Biology

Building 64, Room 248
Tel: 510-486-4225, Fax: 510-486-5909

Lawrence Berkeley Laboratory
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