[phenixbb] ADP high variance

Pavel Afonine pafonine at lbl.gov
Thu Mar 20 07:43:58 PDT 2008

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 

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).


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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