[phenixbb] Exclude Waters from order_solvent=true updates

[Pavel Afonine]

Hi Doeka,

by default all atoms are subject to refinement of coordinates, ADP (iso 
or aniso, depending on the resolution and presence of ANISOU card in 
input file) and occupancy (13+ rules apply, as detailed here: 
https://phenix-online.org/phenixwebsite_static/mainsite/files/newsletter/CCN_2015_07.pdf#page=12 
).

Solvent update option enables adding new water or removing existing 
water based on set criteria.

Pavel

On 11/13/23 19:41, Hekstra, Doeke Romke wrote:
> 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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