[phenixbb] wxu scale in phenix.refine

Pavel Afonine pafonine at lbl.gov
Tue Sep 18 13:30:41 PDT 2007

Hi Jianghai,

phenix.refine writes out the total B-factors after TLS refinement (this 
is why each atom participating in a TLS group receives ANISOU record 
regardless the resolution). The total B is the sum of individual local 
B-factors (isotropic) + TLS contribution (anisotropic).

Now if you take a model previously refined with TLS and refine just 
individual B-factors for this model  (no TLS) then you don't need to do 
anything special to preserve the TLS information from the previous runs 
or read in the TLS matrices. This is simply because this TLS information 
is "stored" in total atomic B-factors (ANISOU records).

One thing here you must be careful about. Like I said above, the model 
after TLS refinement contains ANISOU records. If you take such a model 
for individual B-factors refinement, phenix.refine will think that you 
are going to refine atoms with ANISOU records as individual anisotropic. 
To prevent phenix.refine from doing this you need to explicitly say that 
all atoms must be refined as isotropic (no matter what is in you PDB 
file). Here is how:

% phenix.refine model_after_tls.pdb data.mtz adp.individual.isotropic=all

For more information, details and examples, see new updated 
phenix.refine documentation here:

We will work out something more automatic for this in future (including 
possibility to adjust wxu_scale when TLS is used).

Thanks for your question and, as always, let me know if you have any 
other questions!


Jianghai Zhu wrote:
> I will chime in.  Is it possible for phenix.refine to get the TLS
> parameters from a previous run? then we can change wxu_scale value
> during an individual_adp refinement in the presence of fixed TLS
> parameters.
> Jianghai

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