[phenixbb] Difference Map positive peaks in release dev-798

Pavel Afonine pafonine at lbl.gov
Mon Jun 27 11:20:43 PDT 2011

Hi Engin,

> 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.

I have special handling of "water - other_isolated_non_water_atom" 
situations that in theory should allow shorter distances, but apparently 
this fails sometimes (not always though). I should review that code 
given that I have more practical examples now.


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