[phenixbb] Difference Map positive peaks in release dev-798
Engin Özkan
eozkan at stanford.edu
Mon Jun 27 11:13:44 PDT 2011
On 6/27/11 10:43 AM, Pavel Afonine wrote:
>
> In this case one of the waters needs to be shifted towards green
> density, and you need to add another water to empty blob (I don't know
> why phenix.refine did not add it automatically - I will investigate
> once I get a chance).
Dear Pavel,
This has been my experience with Na sites as well. Phenix.refine
water-update would always move/delete my waters out of coordination
spheres (so I would turn off solvent updates, and strictly restrain
these waters). I always assumed that since Mg and Na coordinate water
with very short distances (2-2.4 Angstroms) compared to water to N and O
atoms, they were disliked by solvent updates. Since I have not looked at
the code (and haven't used the recent versions for Mg/Na containing
structures), I cannot confirm this, but does solvent-update assume
waters should be within 2.3-3.5 A? If that is the case, that may kill
some true water sites.
Cheer,
Engin
--
Engin Özkan
Post-doctoral Scholar
Howard Hughes Medical Institute
Dept of Molecular and Cellular Physiology
279 Campus Drive, Beckman Center B173
Stanford School of Medicine
Stanford, CA 94305
ph: (650)-498-7111
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