[phenixbb] ordered solvent removing metal ion coordination

Engin Ozkan eozkan at stanford.edu
Mon Nov 24 15:16:33 PST 2008


Is there a way to shut off solvent checking for a few waters?  I have 
what looks like sodium-coordinating waters that get taken out by ordered 
solvent filtering, even as I am loosely restraining them to be at 
distances expected for sodium. These waters -I have 4 NCS-related 
copies- are taken out by filtering, which messes up water numbering, and 
makes my restraint descriptions irrelevant.  I have tried putting them 
in a separate chain, but they get fused to the solvent chain by phenix.  
My other option is to describe those waters as a different type of atom 
(not HOH), but they are water molecules, so I am reluctant. And I want 
to keep ordered_solvent True.

For cif files already available in the default ccp4 library, NA seems to 
be elemental sodium, NAW, NA5 and NA6 seem to be specific sodium+water 
complexes with three, five and six waters coordinating (where they are 
no longer HOH, obviously). So, I have created bond/angle restraints 
specifically to my atoms, but is there an easy way to do this? Or should 
I just create a two-water NA (NA2.cif) specific for my case and call 
waters as some O atom? That's easy, but I wonder if that's the common 
practice (or I am missing something completely).

Any ideas?



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