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, Pavel 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 _______________________________________________ phenixbb mailing list [email protected] http://phenix-online.org/mailman/listinfo/phenixbb Unsubscribe: [email protected]