[phenixbb] Adding H atoms onto ligand

[Young-Jin Cho]

Let me excuse to post another similar issue.
I was now modifying AMPPNP ('ANP' in its library name). Although it came from coot/ccp4 library, phenix does not recognize so I had to generate .cif file from the pdb.
 As it turned out AMPPNP is hydrolyzed in the crystal having AMPPN (terminal Phosphate group needs to be removed), I made from coot (simply deleted  atoms) and made another .cif file. One question what I have now is while I am adding H atoms into a whole molecule, how I can add H atoms onto terminal AMPPN (N atom). Unlike ATP case, it is very certain that terminal N atom should have 2 H's.  I did Molprobity as in the general case to add H atoms, but it didn't make it.

Another questions is how I can remove H atoms from the pdb file. I did "phenix.refine model.pdb remove="element H" but got a message as below:
Processing inputs. This may take a minute or two.
Sorry: Ambiguous parameter definition: remove = element H
Best matches:
  refinement.refine.occupancies.remove_selection
  refinement.geometry_restraints.remove.angles
  refinement.geometry_restraints.remove.dihedrals
  refinement.geometry_restraints.remove.chiralities
  refinement.geometry_restraints.remove.planarities

Thanks in advance,

YoungJin


ps. Tanks Nat!