Ed, maybe I didnt understand your idea as well as I thought. If you just want to avoid large B-factor jumps rather than giving B-factors any more meaningful(?) value that is a different story. Certainly fairly easyly done, but probably not high on the priority list. Maybe something for a little script...
B ________________________________________ From: Ed Pozharski [[email protected]] Sent: 04 November 2010 18:17 To: Bernhard Lohkamp Cc: [email protected] Subject: Re: adding residues (feature request?) Bernhard, I think for the loop that is about to close taking the average from flanking residues is good enough. Not sure what you mean by the second example ("last residue has a low B"). I think what causes problems in refmac is a sharp discontinuity, as it contributes greatly to the B-factor restraints. Refinement will adjust B-factors properly if they are higher/lower, but not if they jump from 90 to 20 from residue to residue. The way I adjust B manually is by looking at the B-factor of the next residue, which is not too sophisticated approach and should be easy to implement. Well, in the end it's a minor problem, and easy to fix manually. Cheers, Ed. On Thu, 2010-11-04 at 16:11 +0100, Bernhard Lohkamp wrote: > Dear Ed, > > I think I get your idea, however this is not a straight forward issue I > believe. What do you imagine happens for a loop then? You may end up > connecting a high B residue to a low one when closing it? Does that make > refmac happy? Or your last residue (since it is still well ordered) has > a low B, then you dont gain anything? More appropriate may be a > weighting and adjustment of B-factors based on e.g. real-space CC. But I > guess until we have tools in Coot to refine (or in the first instance > guess) B-factors you better adjust the Bs yourself. Your guess (knowing > the structure and seeing the map) is better than any approximation we > can easily come up with (at least for now). > > My 50 Oere (just fazed out BTW), > > Bernhard > > > When adding residues to the N- or C-terminus, it may be desirable that > > the B-factors of the new residue match that of the previous terminal > > residue. Right now it uses defaults (20 for main chain, 30 for side > > chain) which are sensible fir a well-ordered model, but this causes > > problems with the subsequent refmac run for somewhat disordered regions > > where<B> may be significantly higher. > > > > The current workaround is to modify residue properties manually (or keep > > resetting the defaults). Naturally, the wisdom of adding extra residues > > with<B>~100 is questionable :) > > > > Cheers, > > > > Ed. > > > *************************************************** Dr. Bernhard Lohkamp Assistant Professor Div. Molecular Structural Biology Dept. of Medical Biochemistry and Biophysics (MBB) Karolinska Institutet S-17177 Stockholm Sweden phone: (+46) 08-52487651 fax: (+46) 08-327626 email: [email protected]
