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RE: [ccp4bb]: water picking
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Dear Bernie,
please be careful in simply setting occupancies of questionable water
molecules to zero in CNS! The reason for my warning is that CNS draws a bulk
solvent mask around atoms without taking care of their occupancies. Thus, a
water molecule with occ=0 creates a hole in the bulk solvent mask that then
creates a positive peak in the resulting difference map, errornously
confirming what you've put in! It is better to omit such an atom either by
manual deletion or by not selecting it in the refinement and bulk solvent
calculation (somewhere in the CNS script).
Good luck,
Dirk.
*****************************************************
Dirk Kostrewa
Paul Scherrer Institut e-mail: dirk.kostrewa@psi.ch
Life Sciences phone: +41-56-310-4722
OSRA/007 fax: +41-56-310-4556
CH-5232 Villigen PSI WWW: http://www.sb.psi.ch
Switzerland
*****************************************************
> -----Original Message-----
> From: owner-ccp4bb@dl.ac.uk [mailto:owner-ccp4bb@dl.ac.uk]On Behalf Of
> bds
> Sent: Mittwoch, 13. Juni 2001 16:19
> To: ccp4bb@dl.ac.uk
> Subject: RE: [ccp4bb]: water picking
>
>
> *** For details on how to be removed from this list visit the ***
> *** CCP4 home page http://www.ccp4.ac.uk ***
>
> I agree somewhat with Lawrence. I routinely use water_peak.input in CNS,
> since it screens the neighboring atoms, and updates the molecular
> structure
> file. Then I can reset the occupancy to zero for a water position that I
> don't like, generate maps, etc. before regenerating the molecular
> structure
> file. I always look through the water positions that it's chosen
> to see if
> it's a disordered sidegroup.
>
> I also like to look at the top set of peaks in the difference
> map. Typically
> it will help me identify disordered regions of the structure.
>
> Bernie Santarsiero
>
> Bernard D. Santarsiero
> Senior X-Ray Research Specialist
> Center for Pharmaceutical Biotechnology
> Department of Medicinal Chemistry and Pharmacognosy
> University of Illinois at Chicago
> 3070 MBRB MC 870
> 900 South Ashland Avenue
> Chicago, IL 60607
> Telephone: (312) 413-9304 lab
> (312) 996-5388 office
> FAX: (312) 413-9303
>