[phenixbb] ADP high variance

[Daniel Frey]

Dear Carsten,

the model with the high variance had R and Rfree of 17.8 and 22.2  
(model1)
after switching to wxu_scale 0.01 it was   17.9 and 21.7 (model2) but  
still the adp variance was unacceptable high.
For the next run I set the initial Bfactor of the model to 26 and  
rerun the script, R and Rfree went up to 20.5 and 25.5. Here all ADPs  
were perfect and outliners were not detected in Coot.
Now I am trying to find the optimal weight for wxu_scale, just tried  
to go again higher with the wxu_scale and at 0.1 the adp variance  
still looks fine and the R values dropped to 18.6 and 22.8.

Greetings
Daniel


On Mar 25, 2008, at 6:38 PM, Schubert, Carsten [PRDUS] wrote:

> Daniel,
>
> What was the effect on your R/Rfree?
>
>> -----Original Message-----
>> From: phenixbb-bounces at phenix-online.org
>> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Daniel Frey
>> Sent: Tuesday, March 25, 2008 1:15 PM
>> To: PHENIX user mailing list
>> Subject: Re: [phenixbb] ADP high variance
>>
>>
>> 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
>>
>> _______________________________________________
>> 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