Hi Xplorers, When trying to add unknown atoms to Cyana output PDBs for Xplor use, like HT2/HT3, OT2, or Histidine HD1 or HE2, I noticed coordinates of the patched atoms are funny (visually not in position) in some, if not all, of the PDB files. This makes me wondering how robust is the method implemented in protocol.addUnknownAtoms.
As an example of concerns, I tried to do water refinement on 20 structures after adding unknown atoms and 3 of them blow out. All seems to be caused by added atoms in conflicting with other atoms. Although possibly the structures are not good enough themselves. Nimira
