[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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