[phenixbb] Water molecules whose existence is contingent on the alt conf of a side chain are deleted in refinement

Pavel Afonine pafonine at lbl.gov
Wed Jun 17 17:21:43 PDT 2020

Hi Dale,

currently you can only keep these three water molecules if you disable 
automatic water update (add/remove water).

I wrote water update well before adding sophisticated scenarios for 
occupancy refinement so it isn't aware of these nuances. Clearly it's 
due for revision!

All the best,

On 6/17/20 16:58, Dale Tronrud wrote:
> Hi,
>     I have a model with a Tyr side chain with two conformations.  When it
> is in the A conformation three water molecules occupy the site of the B
> conformation.  I have defined these water molecules to have the alt loc
> A (with no B versions) and set their occupancy equal to that of the A
> version of the Tyr.
>     During refinement, using the GUI, these water molecules disappear
> during the "add/remove water" stage.  My guess is they are running afoul
> of dist_sol_mol_min.  I can't find where I can set this parameter to
> some, very small, value that will allow these waters to live and prosper.
>     If this is my problem, how can I disable this check?
> Dale Tronrud
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