[phenixbb] More stringent water picking
Schubert, Carsten [PRDUS]
CSCHUBER at prdus.jnj.com
Mon Mar 19 10:20:26 PDT 2007
would it be possible to implement the H-bonding criteria? From my experience
with CNS it worked quite nicely. Right now I end up with ~350 waters in a
2.3 A structure of a 30kDa protein, which is a bit much.
From: phenixbb-bounces at phenix-online.org
[mailto:phenixbb-bounces at phenix-online.org]
Sent: Monday, March 19, 2007 1:02 PM
To: PHENIX user mailing list
Subject: Re: [phenixbb] More stringent water picking
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:
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.
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