Daniel, 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: http://www.phenix-online.org/papers/ccp4_july_2005_afonine.pdf That should give you some pointers were to look for tweakable parameters. HTH Carsten ------------------------------------------------------------------------------------------
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? S. PARTHASARATHY AND M.R.N. MURTHY Analysis of temperature factor distribution in high-resolution protein structures Protein Science (1997), 6:2561-2567. http://www.ysbl.york.ac.uk/ccp4bb/2003/msg00432.html http://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0801&L=ccp4bb&T=0&F=&S=&P=52510 J.D. DUNITZ and D.N.J. WHITE Non-rigid-body thermal-motion analysis. Acta Cryst. (1973). A29, 93 Cheers, Pavel. ------------------------------------------------------------------------------------------
-----Original Message----- From: [email protected] [mailto:[email protected]]On Behalf Of Daniel Frey Sent: Thursday, March 20, 2008 7:00 AM To: [email protected] 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
[email protected] Tel: +41446355558
www.biochem.uzh.ch/gruetter www.structuralbiology.uzh.ch
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