[phenixbb] TLS, B factors, phenix and refmac

Mischa Machius Mischa.Machius at utsouthwestern.edu
Tue Apr 1 13:01:37 PDT 2008

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

More information about the phenixbb mailing list