[phenixbb] ADP high variance

[Pavel Afonine]

Hi Daniel,

I'm glad you managed this to work the way you like. However, the 
wxu_scale value looks very small (especially at 1.8A resolution) and 
this fact makes me think that the root of the problem is something else.

Cheers,
Pavel.


Daniel Frey wrote:
> 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
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>
>>>       
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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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