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... 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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