[phenixbb] Ordered solvent in phenix.refine

[Pavel Afonine]

Hi Oliver,

indeed, in recent versions phenix.refine tries to keep existing waters 
as intact as possible, but can remove them if they do not satisfy 
screening criteria.

You can ask the program to keep existing waters unconditionally by using 
"ordered_solvent.keep_existing=true" (also can be set in the GUI).

Pavel

On 2/23/24 08:53, Oliver H. Weiergräber wrote:
> Hello,
>
> after switching from version 1.20 to 1.21, I noticed that the updated 
> list of waters generated by the ordered_solvent option in 
> phenix.refine is no longer numbered sequentially; it seems a final 
> re-numbering step is now skipped. Is this intentional? Of course it 
> can be advantageous to keep waters from changing their numbers, e.g. 
> if they are part of occupancy groups.
> On a related note, is there a mechanism to protect certain "important" 
> waters from being deleted while all the rest is updated as usual? One 
> obvious option would be a dedicated chain ID, but afaik phenix.refine 
> accepts a chain ID for output but not for input waters ...
>
> Best regards,
> Oliver
>
> ==================================================
>   Prof. Oliver H. Weiergräber
>   Institute of Biological Information Processing
>   IBI-7: Structural Biochemistry
>   Forschungszentrum Jülich
>   52425 Jülich, Germany
>   Tel.: +49 2461 61-2028
>   Fax: +49 2461 61-9540
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