Hi Sam,
I'm refining a 2.88 resolution structure and would like to pick waters. I assume the default low_resolution is set to 2.8 Angstroms and so my lower resolution map is not yielding any waters.
Yes, this is correct.
How do I change the resolution cutoff for water picking to be 3.0 Angstroms? I tried adding "refinement.ordered_solvent.low_resolution=3.0" to my command line arguments
This is exactly what you need to do.
and phenix is reading this, but the refinement crashes about 15 seconds in with the message:
================== Extract refinement strategy and selections =================
Sorry: Selection string 'water' results in empty selection (selects no atoms).
I can't tell anything based on the above error message. Can you send me the exact command you used including all parameter files (if any)? Pavel.