[phenixbb] nucleic acid secondary restraints breaking in 1.7.1-743

Nathaniel Echols nechols at lbl.gov
Sun Aug 14 16:29:32 PDT 2011


On Sun, Aug 14, 2011 at 4:26 PM, Francis E Reyes
<Francis.Reyes at colorado.edu> wrote:
> Traceback (most recent call last):
>  File "/usr/local/phenix-1.7.1-743/phenix/phenix/command_line/refine.py", line 11, in <module>
>    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>  File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/command_line.py", line 67, in run
>    overwrite = command_line_interpreter.command_line.options.overwrite)
>  File "/usr/local/phenix-1.7.1-743/phenix/phenix/refinement/driver.py", line 112, in __init__
>    hbond_params=self.params.hydrogen_bonding)
>  File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 494, in create_hbond_proxies
>    log=log)
>  File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/__init__.py", line 286, in hydrogen_bond_proxies_from_selections
>    log=log)
>  File "/usr/local/phenix-1.7.1-743/cctbx_project/mmtbx/secondary_structure/base_pairing.py", line 415, in create_hbond_proxies
>    if distance_values[i][2] != '_':
> IndexError: tuple index out of range
>
> When specifying a single base pair when using secondary_structure nucleic acids restraints

Could you please try the latest nightly build?  This may have been
fixed already.

-Nat


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