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

Dale Tronrud detBB at daletronrud.com
Wed Jun 17 16:58:38 PDT 2020


   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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