[phenixbb] ADP high variance

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Tue Mar 25 10:38:05 PDT 2008


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
> 
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> 




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