[phenixbb] refmac,tlsanl vs TLS, B and anisou
PDAdams at lbl.gov
Sat Mar 29 18:26:30 PDT 2008
- We (the PHENIX developers) are working with the PDB to come up with
streamlined deposition of TLS information for PHENIX. There are
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
to extract the ANISOU records so that R-factors can be calculated.
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
writing something in the iso-B column that they can understand - I
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
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
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
to start interpreting TLS header information.
- I agree that it is best for everyone if we have some clear
deposition and tags that make it clear to anyone looking at files
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
of phenix.refine and REFMAC.
Deputy Division Director, Physical Biosciences Division, Lawrence
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
1 Cyclotron Road
Berkeley, CA 94720, USA.
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