I was running phenix refinement using the following command:
phenix.refine data.mtz model.pdb \ strategy=individual_sites+tls+individual_adp \ my_lib.cif tls.params
the run crashed with the error: ...... ...... File "/usr/local/phenix-1.3-final/mmtbx/mmtbx/monomer_library/pdb_interpretation.py", line 970, in get_lib_link atom_dicts[angle.atom_3_comp_id].get(angle.atom_id_3, None)] IndexError: list index out of range
Is the index error refering to some problem in the reflection file (mtz)?
Most likely the root cause is an error in my_lib.cif. atom_3_comp_id of an angle in a link definition is invalid. We should give you a more helpful error message. Could you send me my_lib.cif and the relevant fragments from your pdb file, i.e. the residues to be linked? Ralf