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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: Eva Kirchner eva {- dot -} kirchner {- at -} UNI-TUEBINGEN {- dot -} DE Date: 2007-04-18 starting to think that my Refmac is somewhat crappy, I tried this before, and then all the B-factors were exactly the same. Now, I tried it again and they are not... Something's still wrong here. (But I'm still curious about the B-factor refinement when there is no "REFI BREF ISOT" in the com-file...) Eva 2007/4/18, Mischa Machius > > Like Harry said, it is not justified to do individual B factor refinement > at that resolution. Well, you can do it, but you'll end up with funny > results, such as what are observing right now. Still, from a pragmatic point > of view, individual B factor refinement in cases like these can have a > positive effect on the electron density. However, keep in mind that the > resulting B factors may physically not be very meaningful. In the end, > you'll have to switch to grouped B factor refinement, or you risk nasty > comments from an attentive mentor or reviewer (and rightly so). Hope that > helps. Best - MM > On Apr 18, 2007, at 7:20 AM, Eva Kirchner wrote: > > 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 > > 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 > > > > > -------------------------------------------------------------------------------- > Mischa Machius, PhD > Associate Professor > UT Southwestern Medical Center at Dallas > 5323 Harry Hines Blvd.; ND10.214A > Dallas, TX 75390-8816; U.S.A. > Tel: +1 214 645 6381 > Fax: +1 214 645 6353 > > > CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007 |
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