[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
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Head, Berkeley Center for Structural Biology
Deputy Principal Investigator, Berkeley Structural Genomics Center

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