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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