[phenixbb] Can the Update Waters routine ignore specified waters?

Engin Özkan eozkan at stanford.edu
Tue Apr 3 09:40:56 PDT 2012

On 4/3/12 9:15 AM, Nathaniel Echols wrote:
> At the very least, it should not be removing waters that have bond restraints.
I second that.

And if not that, there is one thing that I think we all can agree on: 
The routine can remove or add waters, but it should preserve numbering 
of residues that are manually defined as part of some restraint (such as 
one from phenix.metal_coordination). This way you do not start 
restraining HOH-5 to a Na and then at the end of the whole routine have 
HOH-105 next to Na and your restraints trashed. Or have another HOH-5 
that is now 20 A away, unrelated to your Na. I don't know how the 
update-waters routine handles that now. Moreover, it used to be that 
links/restraints from previous GUI runs would be silently kept by 
default, and in your next phenix.refine run, your restraints are just 
plain wrong (I think Nat has changed or is changing that behavior, thanks!).


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