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
little.
- I am in agreement with George (not unusual).
- As far as I remember Garib was supportive of the idea of no longer
depositing
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
parameters
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
displacements).
- 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
atomic
displacements.
- 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
iso-B
column (probably by colouring the atoms by B-factor in a display
program).
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
residual
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
http://cci.lbl.gov/paul
Lawrence Berkeley Laboratory
1 Cyclotron Road
BLDG 64R0121
Berkeley, CA 94720, USA.
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