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Re: [ccp4bb] Stop Refmac from refining B factors? |
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CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007Subject: Re: Stop Refmac from refining B factors? From: Phil Jeffrey pjeffrey {- at -} PRINCETON {- dot -} EDU Date: 2007-04-18 > You should be refining an overall temperature factor at that > resolution. It's one of the choices in the list, instead of "isotropic". I disagree with this. At that (3.2 Angstrom) resolution I've often found than a tightly restrained individual B-factor refinement gives a significantly lower R-free than a single overall B-factor. I also prefer it to grouped B-factors in CNS, because the latter are not geometrically restrained and show a lot of physically unreasonable waywardness (although often, similar R-free as B-individual). Individual B's can also be restrained by non-crystallographic symmetry and as far as I can tell grouped B's are not. I think one has to explore all possibilities rather than take one fixed approach to working at modest resolutions, and the optimal solution is likely to be different for different structures. Phil Jeffrey Princeton, NJ >> Hi, >> >> I have a little problem with B-factor refinement. I'm using the CCP4i >> interface, Refmac 5.2.0019, a resolution of 30-3.2 A (I tried 8-3.2 A >> as well, it doesn't make a big difference for this problem), and a >> current Rfree of 30.4%. >> >> Refmac refines the B-factors so that they are nearly the same for main >> chain and side chain, and I don't like that (or could it make sense in >> any way?). Moreover, my structure is a protein complex, and Refmac is >> mainly doing this for one component of the complex. If I take the >> B-factors from the original uncomplexed protein (around 18, 1.75 A) >> and add 44 to them with moleman to get them in the range they are in >> the complex, Refmac "flattens" them remarkably in only 5 cycles of >> restricted refinement. Does anyone have an explanation for this? I am >> pretty sure that the complex components are in the right place, I see >> beautiful density and everything I should see at this resolution. >> >> Here is what I tried further: >> >> * I de-selected "Refine isotropic temperature factors" in the Refmac >> interface. There was no REFI BREF ISOT any more in the com file. But >> there was also no difference in the B-factors compared to when there >> _was_ REFI BREF ISOT in the com file... So does Refmac just _ignore_ >> my wish not to refine B-factors? (The REFI keywords were as follows: >> type REST - resi MLKF - meth CGMAT - is there any B-factor-thing >> hidden in this?) >> >> * I played around with the geometric parameters. If I select the >> B-factor values there (the keywords are TEMP BFAC >> >> difference, what values I fill in there, the resulting B-factors are >> always the same (but different from when I don't use the TEMP keyword, >> and even "flatter"). Default for WBSCAL is 1.0, I tried 10, 1.0, 0.1, >> 0.01, and the equivalent numbers for the sigbs. >> >> Thanks for any thoughts on this, >> >> Eva > > ------------------------------------------------------------------------- > > Harry M. Greenblatt > > Staff Scientist > > Dept of Structural Biology harry.greenblatt@weizmann.ac.il > > > Weizmann Institute of Science Phone: 972-8-934-3625 > > Rehovot, 76100 Facsimile: 972-8-934-4159 > > Israel > > > CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007 |
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