[phenixbb] changing TLS groups mid refinement

Pavel Afonine PAfonine at lbl.gov
Fri May 14 13:50:46 PDT 2010

Hi Scott,

> I have inherited a refinement project.
> I was not satisfied with the previous choice of TLS groups.
> I used TLSMD to determine a new set of TLS domains.
> Can I just proceed or should I do anything special to the starting PDB to "erase" any influence of the previous choice of TLS groups.

you don't need to do anything special. Just keep going with the new TLS 

Which model did you use for determination of new TLS groups? If you used 
the old one with old ADPs then the new TLS groups are influenced by the 
previous choice of TLS groups. This is because TLSMD uses the ADPs from 
your input PDB file to determine the TLS groups.

Ideally, you need to to the following:

- convert to isotropic and reset to a constant value all B-factors;
- do group ADP refinement with one or two ADP per residue in phenix.refine;
- submit refined model to TLSMD to determine TLS groups;
- throw away this model (the one for which you refined group ADP);
- use you current best available model with the new TLS groups.


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