[phenixbb] index error in phenix refinement

Raja Dey rdey at usc.edu
Wed May 27 10:38:24 PDT 2009


Dear Friends,
                        I was running phenix refinement with the following command:

phenix.refine YCd4p4_output.mtz p53_2.1.pdb simulated_annealing=true main.ncs=true refinement.ncs.excessive_distance_limit=6 ncs_groups.params ncs.find_automatically=False ordered_solvent=true strategy=rigid_body+individual_sites+group_adp+tls rigid_body_selections.params output.write_maps=true output.prefix=may27_1 --overwrite

It ran for a while and then got the following error...
Does anyone have idea what's going wrong?

Traceback (most recent call last):
  File "/usr/local/phenix-1.4-3/phenix/phenix/command_line/refine.py", line 9, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/command_line.py", line 89, in run
    call_back_after_monitor_collect=call_back_after_monitor_collect)
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/driver.py", line 1098, in run
    call_back_after_monitor_collect = call_back_after_monitor_collect)
  File "/usr/local/phenix-1.4-3/phenix/phenix/refinement/strategies.py", line 153, in refinement_machine
    model.show_groups(rigid_body = True, out = log)
  File "/usr/local/phenix-1.4-3/mmtbx/model.py", line 709, in show_groups
    start = i_selection[0]
IndexError: Index out of range.

Thanks...
Raja





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