| Quick navigation: | Home | Site Map || References | Biography || Copyright | Other copyright | Contact us | | |
|
|
Re: [ccp4bb] Stop Refmac from refining B factors? |
|
CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007Subject: Re: Stop Refmac from refining B factors? From: Roberto Steiner roberto {- dot -} steiner {- at -} KCL {- dot -} AC {- dot -} UK Date: 2007-04-18 On 18 Apr 2007, at 14:39, Eva Kirchner wrote: > > > (But I'm still curious about the B-factor refinement when there is > no "REFI BREF ISOT" in the com-file...) Eva, Refmac internal default is REFI BREF ISOT that's why even if you remove the above line from the com file (or deselect that option from the interface) it still does ISOT BREF refinement. It does tell you that though.... if you look at the log file there's a bit that says ....... Method of minimisation : Sparse Matrix Experimental sigmas used for weighting Number of Bins and width: 20 0.0080 Refinement of individual isotropic Bfactors .......... what do you have there when you deselect the B fact option from the interface? I agree with Herman that at 3.2 A isotropic B values refinement can be useful. Roberto > > 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 >> >> 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 > > > ---------------------------------------------------------------------- > ---------- > 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 > > > --- Dr. Roberto Steiner Randall Division of Cell and Molecular Biophysics New Hunt's House King's College London Guy's Campus London, SE1 1UL Phone +44 (0)20-7848-8216 Fax +44 (0)20-7848-6435 e-mail roberto.steiner@kcl.ac.uk CCP4bb navigationCCP4bb <-- 2007 <-- April 2007 <-- 18 April 2007 |
| ProteinCrystallography.org: Copyright 2006-2008 by Quid United Ltd |