[phenixbb] More stringent water picking
Frank von Delft
frank.vondelft at sgc.ox.ac.uk
Mon Mar 19 10:40:41 PDT 2007
Maybe it could be more sophisticated, but it would be a nice start, and
presumably a lot simpler to implement?
phx.
> -----Original Message-----
> From: phenixbb-bounces at phenix-online.org
> [mailto:phenixbb-bounces at phenix-online.org] On Behalf Of Paul Adams
> Sent: 19 March 2007 17:28
> To: PHENIX user mailing list
> Subject: Re: [phenixbb] More stringent water picking
>
> Hi Everyone,
>
> I think it would be sensible to change:
>
> - ordered_solvent.max_solv_macromol_dist to something smaller
> like 3.5A
> (i.e. only look in the first hydration shell).
> - ordered_solvent.secondary_map_cutoff to 1.5 sigma
>
> The CNS h-bond criteria might help, although it I would
> prefer something more sophisticated be done as part of a
> mechanism to distinguish water from ions.
>
> Cheers,
> Paul
>
>
> Pavel Afonine wrote:
>
> > Hi Carsten,
> >
> > thanks for your question!
> >
> > The main water picking criteria in phenix.refine are:
> > 1) Fo-Fc map;
> > 2) 2Fo-Fc map;
> > 3) macromolecule - water distance;
> > 4) water-water distance;
> > 5) B-factors and occupancies max/min values; plus some
> more of expert
> > level ...
> >
> > There is no specific H-bonding criteria implemented. You can play
> > with sigma cutoff for both maps and with the distances
> above. In most
> > of the cases it the reasonable behavior.
> >
> > I would be interested in Paul's (Adams) comments about his
> experience
> > of usefulness of H-bonding criteria in CNS.
> >
> > Thanks!
> > Pavel.
> >
> >
> >
> > Schubert, Carsten [PRDUS] wrote:
> >
> >> Hi,
> >>
> >> is it possible to increase the stringency criteria for
> picked waters,
> >> besides increasing the sigma level? E.G. something on the order of
> >> the H-bonding criterion found in CNS? I find that the automated
> >> water-picking routine gives me quite a few waters, which are not
> >> necessarily justified by visual inspection of the maps.
> >>
> >> Thanks
> >>
> >> Carsten
> >>
> >>
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> >
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> --
> Paul Adams
> Senior Staff Scientist, Physical Biosciences Division Head,
> Berkeley Center for Structural Biology Deputy Principal
> Investigator, Berkeley Structural Genomics Center
>
> Building 64, Room 248
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>
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