I suspect there's not going to be consensus on anything except that
there needs to be a standardization regarding deposited TLS
parameters. Probably the first step is to convince the pdb to not
throw away the record describing what's actually in the B-factor column.
In my (probably unimportant) opinion, I agree that the B value on the
ATOM card should be the equivalent isotropic thermal parameter of the
atom. I personally don't like to see ANISOU records when anisotropic
thermal parameters weren't refined. I agree anisotropic values
derived from TLS are useful, but I'd like there to be a flag on the
ANISOU record, or maybe a different name on the ANISOU record (Yeah,
I know that suggestion won't fly) so that one could distinguish
between refined anisotropic thermal parameters and those derived from
TLS parameters.
If the TLS groups used are contained in the pdb file, I can manage to
generate a close-enough facsimile of the refinement (although not
automatically) so that I can look at the ellipsoids and learn what I
want to learn. Since I'm not a bioinformatics center, this has been,
so far, good enough for me.
Sue
On Mar 29, 2008, at 1:56 PM, George M. Sheldrick wrote:
I think that it is essential that the PDB file that actually gets
deposited contains ANISOU records that have had the isotropic
contributions added already, and that the B on the atom record is
one third of the trace of the orthogonalised Bij tensor that can be
derived from the ANISOU record, just as it is for an anisotropic
refinement without TLS (or a refinement with TLS restraints rather
than constraints, as in the next version of SHELXL, release NOT
imminent). Then if you are not interested in anisotropy you still
have meaningful B values on the ATOM record, and a structure factor
calculation (e.g. with SFCALC) will get the R factors right. If I
have understood the rather convoluted discussion on this question,
phenix.refine does this correctly, but if you use REFMAC you need
to use another program (TLSANL ?) to convert the PDB file before
you deposit it. Apparantly many people have forgotten to do this
and the RCSB/EBI has unfortunately not checked it (which would
be trivial for them to do). If they could be persuaded to check
that the ATOM and ANISOU records are consistent as explained above,
the problem would sort itself out, at least for new depositions.
George
Prof. George M. Sheldrick FRS
Dept. Structural Chemistry,
University of Goettingen,
Tammannstr. 4,
D37077 Goettingen, Germany
Tel. +49-551-39-3021 or -3068
Fax. +49-551-39-2582
On Sat, 29 Mar 2008, Pavel Afonine wrote:
Hi Frank,
Hi Frank,
All your reasons are there for the convenience of the
*crystallographer*,
mine are for the end user (=unsuspecting biologist) -- who
doesn't know TLS
even exists (none of used to), never mind about Hirshfeld's test
and how it
relates to TLS (I didn't), and certainly not how run it (I still
don't).
This is exactly what phenix.refine does: it puts all together so
you are not
expected to have any knowledge about magic TLS matrices in PDB
file header,
about right programs to convert one into another and so on. In
contrast, if
one split things apart:
- you must know that what's in ATOM record is incomplete;
- you must know that there are TLS matrices that you have to
convert to
appropriate B and add to residual ones;
- you must know that there are the programs out there to do that;
- and you must know how to use these programs too.
So, having complete record doesn't require any manipulations on
the model (and
so extra knowledge) .
Imagine the situation when you got a model with partial B-factors
and another
part encoded in PDB header as TLS and you want to do a refinement
in SHELXL.
In this case you will need to compute the total B to start with
the correct
values. In contrast, if the values are complete, you do not need
to do
anything.
In the end what's important I believe is that the output
information is
clearly accompanied with the explanations about what it represents
and that
there are tools available from both ends (phenix, ccp4) to easily
go from
partial to total and back. The rest is the matter of personal
preferences.
Cheers,
Pavel.
---
Pavel V. Afonine, Ph.D.
Lawrence Berkeley National Lab, Berkeley CA, USA (http://
www.lbl.gov/)
CCI: Computational Crystallography Initiative (http://cci.lbl.gov/)
PHENIX (http://phenix-online.org/)
Sue Roberts
Department of Biochemistry & Molecular Biophysics
University of Arizona
[EMAIL PROTECTED] 520 621-8171
