 |
 |
This is a personal preference. I do model at low sigma levels if there IS some indication of where to put atoms, always try to keep the correct sequence even if some atoms are missing, and just for coot convenience keep atoms with occ = 0, rather than delete them altogether. (COOT will refine a residue with occs = 0, but not one where atoms are missing.. Paul?? Why not!) At deposition the wwwPDB are welcome to (and I think do) strip out all ocs=0.. Eleanor On Mar 26 2012, Gregory Bowman wrote: > 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) >[log in to unmask] >http://www.jhu.edu/bowmanlab > > -- Professor Eleanor Dodson YSNL, Dept of Chemistry University of York Heslington YO10 5YW tel: 00 44 1904 328259 Fax: 00 44 1904 328266