[phenixbb] covalently linked ligand

[Joerg Standfuss]

Dear phenix users,

I am currently building a model where the ligand is linked via schiff  
base to a lysine residue.
To let phenix know about the link I provide the ligand.cif file and  
created the link parameter file as described in the manual. The type  
of link I defined with Jligand as it does not appear in the standard  
ccp4 library. Unfortunately phenix.refine stops with the error  
message below when I provide the so created files. It seems phenix  
has problems to apply the needed ligand modifications ie removing  
hydrogens and oxygens and stops with the refinement. I have no idea  
why this doesn't work and am getting a little desperate so any  
suggestions how to do this properly would be greatly appreciated.  
Could I use for example elBOW to create the link description?

many thanks,

Joerg


   File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ 
monomer_library/pdb_interpretation.py", line 499, in __init__
     mod_mod_id=self.mon_lib_srv.mod_mod_id_dict[apply_data_mod])
   File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ 
monomer_library/pdb_interpretation.py", line 771, in apply_mod
     mod_mon = self.monomer.apply_mod(mod_mod_id)
   File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ 
monomer_library/cif_types.py", line 339, in apply_mod
     result.delete_atom_in_place(mod_atom.atom_id)
   File "/lmb/home/public/xtal/Phenix/phenix-1.4-3/mmtbx/ 
monomer_library/cif_types.py", line 244, in delete_atom_in_place
     raise RuntimeError("delete_atom_in_place: unknown atom_id: %s" %  
atom_id)
RuntimeError: delete_atom_in_place: unknown atom_id: H151

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