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
[email protected] Tel: +41446355558
www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch
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Daniel Frey Department of Biochemistry University of Zurich Winterthurerstrasse 190 8057 Zurich Switzerland
[email protected] Tel: +41446355558
www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch
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