Hi Luca,
You should find that the hydrogens in the mmCIF file output by Refmac are
flagged as riding hydrogens, not as an explicit part of the model. This
behaviour is as intended, and should not pose a problem for deposition. They
are not in the output PDB file because there is no way to flag
Dear Rens,
CCP4i2 now contains a CIF dictionary accumulator, which should help with
handling such problems (note it's also available as standalone to be used via
command line if that's useful). This is used automatically when providing
multiple ligand CIF dictionaries to the Refinement interfac
Dear Gerlind,
I'm glad that we were of help! I should point out that the "Make link (click 2
atoms)" is dangerous as it only generates a LINK record but not a full link
dictionary - it should only be used for common known links that are present in
the monomer library. This issue is discussed in
Dear Gerlind,
Where did you get your mad_monlib.cif file? It shouldn't be neccesary for you
to be manually modifying such restraint dictionaries (any more). You can
generate these using AceDRG, either via CCP4i2 or Coot.
Shameless plug:
https://journals.iucr.org/d/issues/2021/06/00/ir5021/index
