[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.


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

More information about the phenixbb mailing list