[phenixbb] ADP high variance

Daniel Frey freyd at bioc.unizh.ch
Tue Mar 25 10:15:06 PDT 2008


Dear Pavel and Carsten,

I finally managed to change the ADP variance by setting the wxu_scale  
below 0.02. Thanks for the advise

Daniel

On Mar 20, 2008, at 3:43 PM, Pavel Afonine wrote:

> Hi Daniel,
>
> Carsten is right, phenix.refine uses a different approach. However,
> changing the wxu_scale should visibly change the ADP variances.
>
> - are you using TLS?
> - what is the exact command you run?
> - if your PDB file has segment identifiers, are they all consistent  
> (no
> mixes)?
>
> Normally, changing the wxu_scale has to change the ADP variances. If  
> it
> does not change then something is not right somewhere. I need some  
> more
> information to tell you exactly what's happening. If you want me to
> debug it some more, I'm happy to do so but I will need to reproduce  
> this
> problem on myself on computer (meaning I need the model and data).
>
> Thanks!
> Pavel.
>
>
> Daniel Frey wrote:
>> Hello,
>> I have a good data set to 1.8 A and refined it with the actual  
>> version
>> of phenix, including annealing and isotropic bfactors. Checking the B
>> factor variance in coot revealed high differences in about 50%  of  
>> the
>> residues. Most of them are at the surface, but still there are
>> residues like phenylalanines and valines within the core where the
>> bfactors jump from 25 to 50 from one carbon atom to the other.
>> Changing wu and wxu_scale did not improve the results. A quick check
>> with refmac improved the results, so i guess I am missing the right
>> restraints for phenix. Which parameters should be changed to improve
>> the bfactor variance in phenix?
>>
>> Thanks for your help
>>
>>
>> Daniel
>>
>> Daniel Frey
>> Department of Biochmistry
>> University of Zurich
>> Winterthurerstrass 190
>> 8057 Zurich
>> Switzerland
>>
>> freyd at bioc.unizh.ch
>> Tel: +41446355558
>>
>> www.biochem.uzh.ch/gruetter
>> www.structuralbiology.uzh.ch
>>
>> _______________________________________________
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>>
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Daniel Frey
Department of Biochemistry
University of Zurich
Winterthurerstrasse 190
8057 Zurich
Switzerland

freyd at bioc.unizh.ch
Tel: +41446355558

www.biochem.uzh.ch/gruetter
www.structuralbiology.uzh.ch




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