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 <[log in to unmask]>
> 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: [log in to unmask]
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