Dear all, I don't know how closely this relates to what James pointed at, but regarding the aspect of NCS information usage in the heavy-atom finding/refinement stage, I would like to mention two programs of my knowledgethat are able to detect NCS in a set of putative heavy atom sites froma substructure solution trial: Professs (CCP4) and SitCom. Probaby I missed others ...
These are useful in particular for cases like heavy atom-soaked structures, where site occupancies are partial and hence peak heights a weak indicator ofcorrectness, but the binding sites are not "random" i.e. still comply to the NCS. Both programs are based on the identification of matching triangles among HA sites. (meaning that the approach is less suited for cases with less than 3 sites per monomer). SitCom extracts HA site matches, no matter whether (closed) rotational NCS or purely translational NCS is present; and it can try to determine an unknown NCS order or apply an expected one. No matter which program used, the main benefit in my opinion is telling correct sites (NCS-conform) from wrong ones, so that ideally the filtering results in an improved substructure and HA phase set. Kind regards, Fabio Am 1/23/14 1:00 AM, schrieb CCP4BB automatic digest system:
Date: Tue, 21 Jan 2014 18:24:34 -0800 From: James Holton <jmhol...@lbl.gov> Subject: Re: Phasing with Many Monomers/AU [...] but your initial problems are going to be phasing. Ideally what you'd want is a way of folding back NCS information into the heavy atom finding and phase refinement process, but I know of no programs that actually do that. In fact, both molecular replacement and heavy-atom finding are hindered by this "pseodo-translation" rather than helped by it. Personally, I blame the fact that methods developers seldom get their hands on "interesting" datasets like yours. [...]
-- Dr. rer. nat. Fabio Dall'Antonia European Molecular Biology Laboratory c/o DESY Notkestraße 85, Bldg. 25a D-22603 Hamburg phone: +49 (0)40 89902-178 fax: +49 (0)40 89902-149 e-mail: fabio.dallanto...@embl-hamburg.de
