[phenixbb] IndexError

Huiying Li hli at crystal.bio.uci.edu
Thu Mar 19 13:39:19 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)?

Thanks for any suggestions.

Huiying Li, Ph. D
Department of Molecular Biology and Biochemistry
Natural Sciences I, Rm 2443
University of California at Irvine
Irvine, CA 92697, USA
Tel: 949-824-4322(or -1953);  Fax: 949-824-3280
email: hli at uci.edu

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