But what about the issue of resolution? As was previously pointed out, at say 3.2 Å resolution, many side chains will fail to fit, but it doesn't seem appropriate to trim them all down. The users need to also be aware of the quality/resolution of the structures that they are looking at.
Greg On Mar 26, 2012, at 9:28 AM, Ed Pozharski wrote: > I agree with Eleanor 100%... > > In my biased opinion, only the atoms supported by electron density > should be included in deposited models. To satisfy the "but this will > mess up the electrostatic potential coloring" argument (a valid one, of > course), the "projected model" can be deposited alongside which must be > clearly advertised as the unconstrained interpretation by the > structure's author. > > Cheers, > > Ed. > > On Sun, 2012-03-25 at 08:36 +0100, Eleanor Dodson wrote: >> As Garib says - an atom with occupancy 0.00 is treated as a marker - >> useful >> for coot - but is not included in any X-ray refinement at all.. Maybe >> it >> would be more aesthetic to maintain geometry but as crystallographers >> I >> think we should be interested in the fit of model to experiment - >> right? - >> and not in reporting a pseudo fit related to geometric parameters >> only.. > -- > Oh, suddenly throwing a giraffe into a volcano to make water is crazy? > Julian, King of Lemurs -- Department of Biophysics Johns Hopkins University 302 Jenkins Hall 3400 N. Charles St. Baltimore, MD 21218 Phone: (410) 516-7850 (office) Phone: (410) 516-3476 (lab) gdbow...@jhu.edu http://www.jhu.edu/bowmanlab
