[phenixbb] High B-factors after Phenix restrained refinement

Steiner, Roberto roberto.steiner at kcl.ac.uk
Fri Dec 16 08:20:14 PST 2011

Hi Nat

The PDBe used to do the conversion automatically (likely still does)

After submission they would send you something like this:

>The PDB no longer accepts or releases entries 
>that contain only residual B-factors. For this reason your entry was 
>converted to full B-factors and ANISOU records encoding the TLS 
>parameters using the protocol as given in:
>The converted file was then run against EDS refinement and as no change 
>was observed in the calculated R-factors, this was considered for release.


On 16 Dec 2011, at 16:11, Nathaniel Echols wrote:

> On Fri, Dec 16, 2011 at 7:54 AM, Da Duan <2dd13 at queensu.ca> wrote:
>> I was just looking at the average B in the refinement log files from Refmac
>> and Phenix Refine. Thanks for the clarification on how Refmac and Phenix
>> calculate the average B. My next question is when depositing the structure,
>> is it more common to deposit structures with the "residual" B-factors or
>> B-factors generated by Phenix that includes the TLS and Ucryst contribution?
>> I also performed sfcheck and the average B generated by the Wilson plot is
>> ~100 which seems to suggest that the Phenix average B is probably "more"
>> correct?
> I had thought that the PDB automatically converted Refmac PDB files to
> contain full B-factors, but the link Ed posted suggests otherwise.  If
> you are depositing the output file from Phenix, at least, you do not
> need to take any additional steps.
> -Nat
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Roberto Steiner, PhD
Randall Division of Cell and Molecular Biophysics Group Leader
King's College London

Room 3.10A 
New Hunt's House 
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Tel 0044-20-78488216
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roberto.steiner at kcl.ac.uk

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