[phenixbb] index error in phenix refinement

Pavel Afonine PAfonine at lbl.gov
Wed May 27 10:49:24 PDT 2009

Hi Raja,

the code where this error happens is very complex and there is no way I 
debug it without reproducing this crash myself. For this I need the 
model, data and exact command you used that leads to this failure.

Could you please send it to me (to my email address, not to the whole 

As always, all the files will be kept confidentially.


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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