[phenixbb] Exclude Waters from order_solvent=true updates

[Hekstra, Doeke Romke]

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: phenixbb-bounces at phenix-online.org <phenixbb-bounces at phenix-online.org> On Behalf Of Pavel Afonine
Sent: Monday, November 13, 2023 3:13 PM
To: Schulz, Dr. Eike <eike.schulz at uni-hamburg.de>; phenixbb at phenix-online.org
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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