[ccp4bb]: Another refmac/tlsanl TLS question

[Ethan Merritt <merritt@u.washington.edu>]

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Another thing I don't quite understand...

The Biso values in the pdb file output by refmac5 after TLS refinement 
are quite different from the Biso values output by tlsanl after 
converting the TLS description into individual ADP records starting 
from that very same refmac5 pdb file.

I realize that the Uij parameterization is only an approximation to
the actual atomic scattering described by Biso+TLS, but I would
expect the Uij parameterization to be chosen so that _something_
came out the same, and Biso (a.k.a. Beffective) is the logical
quantity to hold constant.

- What exactly is the quantity stored in the Biso field of ATOM records
  output by refmac5 after TLS refinement?

- What is being fit (or minimized?) by tlsanl when it converts the
  refmac5 output into a description of individual atomic ADPs?

- If I shouldn't expect Biso to be the same before and after running
  tlsanl, then what should I expect?  Should it get larger? smaller?
  Does the direction or magnitude of change tell me anything about
  the nature of the TLS model?


-- 
Ethan A Merritt       merritt@u.washington.edu
Biomolecular Structure Center Box 357742
University of Washington, Seattle, WA 98195
phone: (206)543-1421
FAX:   (206)685-7002