[phenixbb] More stringent water picking

[Pavel Afonine]

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
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>   
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://phenix-online.org/pipermail/phenixbb/attachments/20070319/bf0f6377/attachment-0004.htm>