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
I think you can change
refinement.ordered_solvent.primary_map_cutoff
from 3 to 3.5 or 4 maybe
and maybe raise
refinement.ordered_solvent.secondary_map_cutoff
to 1.5 or so.
I think this will work:
phenix.refine secondary_map_cutoff=<whatever> primary_map_cutoff=<whatever> <other keywords>
HTH
Peter
----- Original Message -----
From: "Schubert, Carsten [PRDUS]"
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- pickingroutine gives me quite a few waters, which are not necessarily justified by visual inspection of the maps.
Thanks
Carsten
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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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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------------------------------------------------------------------------
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- 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/ Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. --
Maybe it could be more sophisticated, but it would be a nice start, and presumably a lot simpler to implement? phx.
-----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of Paul Adams Sent: 19 March 2007 17:28 To: PHENIX user mailing list Subject: Re: [phenixbb] More stringent water picking
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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----------------------------------------------------------------------
--
_______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
-- 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/
Lawrence Berkeley Laboratory 1 Cyclotron Road BLDG 64R0121 Berkeley, CA 94720, USA. -- _______________________________________________ phenixbb mailing list [email protected] http://www.phenix-online.org/mailman/listinfo/phenixbb
participants (5)
-
Frank von Delft -
Paul Adams -
Pavel Afonine -
Petrus H Zwart -
Schubert, Carsten [PRDUS]