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

Filip YABUKARSKI fyabukar at embl.fr
Mon Jul 2 09:47:59 PDT 2012


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


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