[phenixbb] More stringent water picking
Paul Adams
PDAdams at lbl.gov
Mon Mar 19 10:28:28 PDT 2007
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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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
Tel: 510-486-4225, Fax: 510-486-5909
http://cci.lbl.gov/
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