I've got a couple of instances where I have non-standard amino acids,
nevertheless present in the monomer dictionary, that have additional
non-peptide covalent linkages. I've figured out how to define these,
but if I opt to output hydrogens as a diagnostic I see that Refmac
doesn't delete the ligand hydrogens that were present at the linkage point.
Nothing catastrophic happens in refinement but extra atoms lying along
other covalent bonds makes me a little queasy.
Is there something (non-obvious) in additional user-defined .cif library
that I can use to do this ? Do I simply define a new version of the
monomer (w/o errant hydrogen) and hope that it overwrites the previous
definition ?
I'm doing this at borderline atomic resolution.
Thanks
Phil Jeffrey
Princeton
