[phenixbb] More stringent water picking

Pavel Afonine pafonine at lbl.gov
Mon Mar 19 10:01:57 PDT 2007

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.


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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