Hi,
I am wondering if Refmac version 5.8 is suitable for refining occupancies of a ligand reliably in a ligand-protein complex. I have heard that in older versions there used to be some instability if refining occupancies and B-factors together. Is that still the case? If I try fixing B-factors during refinement would the following shell script below do the job (chain X is for the ligand)? After running the refinement occupancies for the ligand come out refined. But unexpectedly, so do the B-factors as far as I can tell.
Many thanks,
Robert
#!/bin/bash
#
refmac5 HKLIN data.mtz XYZIN model.pdb LIBIN ligands.dict << eof
make refi bfac none
occupancy group id 1 chain X
occupancy refine
eof
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