[phenixbb] Default anisotropic B-factor refinement in phenix.refine?

Pavel Afonine pafonine at lbl.gov
Mon Jul 2 09:58:58 PDT 2012

Hi Filip,

phenix.refine manual may need an update..

At 3A resolution if you run two consecutive refinements first with TLS 
and the next one without TLS then in the second run anisotropic ADPs 
will be converted to isotropic automatically. This is done by 
phenix.refine to prevent accidental refinement of individual anisotropic 
ADPs in such cases. The keyword and threshold are: 


On 7/2/12 9:47 AM, Filip YABUKARSKI wrote:
> Hello,
> I recently started to refine a structure with phenix.refine for a 
> first time. It is a 3A dataset with NCS of 8. For the refinement i 
> wanted to use TLS groups as well as individual B-factors 
> (data/parameter ratio should be fine with ncs of 8) and after several 
> cycles of refinement i get the Rfac of 20 and Rfree of 24 which is 
> quite good (i also use simulated annealing, Secondary structure 
> restraints and NCS restraints). Re-reading the refinement manual I 
> realized that by using a PDB file which comes from a phenix.refine 
> with TLS in the next refinement i am probably doing an anisotropic 
> B-factor refinement for each atom, which in my case is not justified. 
> I found a post on ccp4bb from 19 Fev 2009 discussing this issue but 
> for me it is still not very clear. By reading the PDB i got from 
> phenix.refine (version 1.7.3) it is not very clear (at least for me) 
> if the refinement was with TLS groups and individual isotropic 
> B-factors or with anisotropic B-factors. Basically my question is: if 
> the input PDB has already anisoU records from a previous phenix.refine 
> with TLS groups is the new phenix.refine going to use isotropic 
> individual B-factors or anisotropic ones? (Even if in my case one can 
> assume that i can probably use anisotropic B-factor refinement (24000 
> unique reflections with ncs of 8 vs. 6000 atoms in total) this is 
> rarely the case for non-atomic resolution datasets) I would be very 
> happy if someone gives an explanation. Many thanks
> Cheers
> Filip

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