[phenixbb] Exclude Waters from order_solvent=true updates

[Schulz, Dr. Eike]

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 <pafonine at lbl.gov <mailto:pafonine at lbl.gov>>
Date: Monday, 13. November 2023 at 21:12
To: ESCHULZ <eike.schulz at uni-hamburg.de <mailto:eike.schulz at uni-hamburg.de>>, "phenixbb at phenix-online.org <mailto:phenixbb at phenix-online.org>" <phenixbb at phenix-online.org <mailto: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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