[phenixbb] ADP high variance

Schubert, Carsten [PRDUS] CSCHUBER at prdus.jnj.com
Thu Mar 20 05:55:21 PDT 2008


this appears to be a common thread on this BB, since phenix seems to handle these things quite differently than CNS and refmac(?). A while back I had a similar exchange with Pavel about this. He pointed me to some literature which highlights some of the challenges associated with restrained B-factor refinement using medium to low resolution data. From what I understand the implementation in PHENIX is based on the ideas of Ian Tickle. 
Here is also a paper I found useful:

That should give you some pointers were to look for tweakable parameters. 



> Does anyone know a publication which covers theoretical B-factor distributions?

Here are a few links related to your question that came to my mind first:

D. E. Tronrud
J. Appl. Cryst. (1996). 29, 100-104
Knowledge-Based B-Factor Restraints for the Refinement of Proteins

F. L. Hirshfeld
Acta Cryst. (1976). A32, 239-244
Can X-ray data distinguish bonding effects from vibrational smearing?

Analysis of temperature factor distribution
in high-resolution protein structures
Protein Science (1997), 6:2561-2567.



Non-rigid-body thermal-motion analysis.
Acta Cryst. (1973). A29, 93



> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org]On Behalf Of Daniel Frey
> Sent: Thursday, March 20, 2008 7:00 AM
> To: phenixbb at phenix-online.org
> Subject: [phenixbb] ADP high variance
> 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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