[phenixbb] index error in phenix refinement

Pavel Afonine PAfonine at lbl.gov
Wed May 27 13:47:29 PDT 2009

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:

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.


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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