For my curiosity--are ordered water molecules refined during XYZ and/or ADP refinement in the absence of an ordered solvent update? Best, Doeke -----Original Message----- From: [email protected] On Behalf Of Pavel Afonine Sent: Monday, November 13, 2023 3:13 PM To: Schulz, Dr. Eike ; [email protected] Subject: Re: [phenixbb] Exclude Waters from order_solvent=true updates Hi Eike, in recent versions of Phenix you should be able to use ordered_solvent.keep_existing parameter. By default it is set to False meaning all input water is subject to inspection by the program and can potentially be removed. Setting it True will keep input water no matter what. Pavel On 11/8/23 22:50, Schulz, Dr. Eike wrote:

Hello everyone,

I am refining a few structures via a bash script using constrained occupancy refinement by providing a parameter file. I am trying to model the occupancy of a ligand and the water molecules in its vicinity. This works generally well, but as soon as I switch on ordered_solvent=true, these water molecules are also filtered / updated and eventually removed.

How can I avoid this ? That is specifically excluding a number of water molecules from being updated ?

With best regards,

Eike

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Hi Pavel, thanks a lot - that's really helpful. In the meantime, I found a workaround by semi-manually re-adding the waters in question and then refining without water update, but of course this is (much) more elegant. Thanks again and best regards, Eike -----Original Message----- From: Pavel Afonine mailto:[email protected]> Date: Monday, 13. November 2023 at 21:12 To: ESCHULZ mailto:[email protected]>, "[email protected] mailto:[email protected]" mailto:[email protected]> Subject: Re: [phenixbb] Exclude Waters from order_solvent=true updates Hi Eike, in recent versions of Phenix you should be able to use ordered_solvent.keep_existing parameter. By default it is set to False meaning all input water is subject to inspection by the program and can potentially be removed. Setting it True will keep input water no matter what. Pavel On 11/8/23 22:50, Schulz, Dr. Eike wrote:

Hello everyone,

I am refining a few structures via a bash script using constrained occupancy refinement by providing a parameter file. I am trying to model the occupancy of a ligand and the water molecules in its vicinity. This works generally well, but as soon as I switch on ordered_solvent=true, these water molecules are also filtered / updated and eventually removed.

How can I avoid this ? That is specifically excluding a number of water molecules from being updated ?

With best regards,

Eike

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