[phenixbb] IndexError

Ralf W. Grosse-Kunstleve rwgk at cci.lbl.gov
Thu Mar 19 14:13:12 PDT 2009

> 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?


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