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

Filip YABUKARSKI fyabukar at embl.fr
Mon Jul 2 10:30:41 PDT 2012

Hello again,

First thank you very much for the response

But in this case after the second run of phenix.refine i will lose the 
TLS contribution and the anisoU lines (?). How am I supposed to continue 
with TLS then (given it lowers my R factors i would be happy to keep it) 
and be sure that i do not refine anisotropic ADPs? Or you mean that i 
can do the 2 consecutive runs (with and without TLS) in the end of the 
refinement? Sorry if I got something wrong


On 2012-07-02 18:58, Pavel Afonine wrote:
> 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:
> switch_to_isotropic_high_res_limit=1.5.
> Pavel
> 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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