I think what you describe below is a bit of re-inventing the wheel (in
some sense, not completely). Here is why:
phenix.refine has an extremely complex algorithm of refinement ADP. By
refining ADP I mean refining of all U=Utls+Ucryst+Uresidual. Briefly:
- it does some group iso B refinement to get starting TLS values;
- then it "simultaneously" refines TLS parameters and residual B;
- then it extracts TLS components from total B as described in
http://www.ccp4.ac.uk/newsletters/newsletter45.pdf;
- it monitors to make sure that all parameters are meaningful at all times;
- then it repeats the whole process at next macro-cycle.
Look TLS related code in phenix.refine for more details.
The all details and parameters of the above algorithm were highly
optimized using systematic re-refinement of 355 models selected from
PDB. This makes ADP refinement (TLS+B+etc) in phenix very stable. See
dedicated slide here, for actual results:
http://phenix-online.org/download/documentation/cci_apps/phenix_refine_quick_facts.pdf
At some point, I re-refined all models in PDB (that have data) using TLS
refinement option in phenix.refine. It never crashed or got "unstabale".
So, I don't think there is anything to improve in terms of stability of
TLS refinement in PHENIX.
Please let me know if you find a case where this algorithm implemented
in phenix.refine fails and I will try to fix it asap.
Cheers,
Pavel.
On 4/1/2008 1:01 PM, Mischa Machius wrote:
Hi - Prompted by the recent discussions on B values, TLS refinement
and differences between Phenix and refmac, we looked into these
matters in more detail. We found that the crux of the problem lies in
the fact that TLS and B value refinements are usually decoupled. We
have developed a formalism that rolls both TLS and B value refinement
into one. Phenix and refmac were modified to carry out the
calculations, and the outputs from both programs were made compatible
to allow proper comparison of the results.
We found that the stability of the refinements is now vastly improved.
More importantly, however, due to the reduced number of parameters,
these calculations can be carried out to resolutions of 7 Å with
meaningful representations of indiviual, anisotropic atomic
displacement parameters. This low-resolution limit required
reformulating the calculation of Wilson B values, but that is only a
minor aspect of our treatment that can be neglected.
The new, combined procedure for the simultaneous refinement of TLS/B
is called 'TBS' refinement, reflecting all required components:
Translation, Bibation, Screw.
Interestingly, the ‘T’ component is fairly insensitive to input
parameters, whereas the overall quality of the refinement is greatly
dependent on the ‘B’ component. The more emphasis is put on ‘B’, the
more convincing the results. There is a limit, though. At very high
levels of ‘B’, the so-called ‘bibacity limit’, the refinement becomes
very unstable, leading to inversion in severe cases. Seasoned
crystallographers familiar with the concepts can successfully push the
procedure to quite high 'B limits', whereas less experienced
practitioners should follow the protocols very carefully.
Please contact us for any details.
Best - MM
--------------------------------------------------------------------------------
Mischa Machius, PhD
Associate Professor
UT Southwestern Medical Center at Dallas
5323 Harry Hines Blvd.; ND10.214A
Dallas, TX 75390-8816; U.S.A.
Tel: +1 214 645 6381
Fax: +1 214 645 6353
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