Hi Raja, the problem is that you have an empty selection for a rigid group in your rigid_body_selections.params file: "rigid_body = chain E and chain F". Indeed, if I do: phenix.pdb_atom_selection p53_2.1.pdb "chain E and chain F" it will tell it: (...) chain E and chain F 0 atoms selected The newer version of phenix.refine will not crash but it will stop with this message (I just tried): (...) ================== Extract refinement strategy and selections ================= Sorry: Empty selection. (...) So, it's probably a good idea to update to the latest version: http://www.phenix-online.org/download/ Regarding your selection, you probably meant "chain E or chain F" (and not "chain E and chain F") assuming that chains E and F form one rigid body. Pavel. On 5/27/09 10:38 AM, Raja Dey wrote:
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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