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 _____ 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: [email protected]
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
participants (2)
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Huiying Li -
Ralf W. Grosse-Kunstleve