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<TITLE>More stringent water picking</TITLE>
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<DIV><SPAN class=384501517-19032007><FONT face=Arial color=#0000ff>Thanks
Guys,</FONT></SPAN></DIV>
<DIV><SPAN class=384501517-19032007><FONT face=Arial
color=#0000ff></FONT></SPAN> </DIV>
<DIV><SPAN class=384501517-19032007><FONT face=Arial color=#0000ff>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.</FONT></SPAN></DIV>
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<DIV class=OutlookMessageHeader dir=ltr align=left><FONT face=Tahoma
size=2>-----Original Message-----<BR><B>From:</B>
phenixbb-bounces@phenix-online.org
[mailto:phenixbb-bounces@phenix-online.org]<BR><B>Sent:</B> Monday, March 19,
2007 1:02 PM<BR><B>To:</B> PHENIX user mailing list<BR><B>Subject:</B> Re:
[phenixbb] More stringent water picking<BR><BR></FONT></DIV>Hi
Carsten,<BR><BR>thanks for your question!<BR><BR>The main water picking
criteria in phenix.refine are:<BR>1) Fo-Fc map;<BR>2) 2Fo-Fc map;<BR>3)
macromolecule - water distance;<BR>4) water-water distance;<BR>5) B-factors
and occupancies max/min values;<BR>plus some more of expert level
...<BR><BR>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.<BR><BR>I would be interested in Paul's
(Adams) comments about his experience of usefulness of H-bonding criteria in
CNS.<BR><BR>Thanks!<BR>Pavel.<BR><BR><BR><BR>Schubert, Carsten [PRDUS] wrote:
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<P><FONT face=Arial>Hi,</FONT> </P>
<P><FONT face=Arial>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. </FONT></P>
<P><FONT face=Arial>Thanks</FONT> </P>
<P> <FONT
face=Arial>Carsten</FONT> </P><BR><PRE wrap=""><HR width="90%" SIZE=4>
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