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On Thu, Jan 11, 2007 at 12:33:37PM +0100, [EMAIL PROTECTED] wrote: > > Likewise, the argument that disordered atoms will inflate the B > > factors of the ordered atoms (like James Irving mentioned) is valid > > the other way around too: an ordered C-beta will keep the B factor > > for C-gamma at bay, and so on. If the B factor is meant to reflect > > degree of disorder, then a mutual effect is completely desirable. > > However, we all know that B factors are not perfect, either. > > As has been mentioned in a previous email, the current B-factor > restraints on e.g. lysine side chains are far too restrictive. Since the > CA-CB bond is rotatable, the CG atom can be anywhere on a cone around > the CB, while the CB itself stays exactly in place. This effect is > clearly visible in many high-resolution structures where the CB is often > perfectly visible with no electron density whatsoever visible beyond > that. In my opinion, the B-factor restraints of the major refinement > packages should be adapted to make a distinction between rotable and > non-rotatable bonds. This makes physically far more sense than the > current distinction between main chain/side chain restraints and the > artifacts mentioned above would no longer occur. > Just as an FYI, Dale Tronrud proposed something to this effect awhile ago and implemented it in TNT: http://scripts.iucr.org/cgi-bin/paper?wb0026 -Tim -- --------------------------------------------------------- Tim Fenn [EMAIL PROTECTED] Stanford University, School of Medicine James H. Clark Center 318 Campus Drive, Room E300 Stanford, CA 94305-5432 Phone: (650) 736-1714 FAX: (650) 736-1961 ---------------------------------------------------------
