[phenixbb] nucleic acid secondary restraints breaking in 1.7.1-743
Francis E Reyes
Francis.Reyes at Colorado.EDU
Mon Aug 15 06:04:56 PDT 2011
Thanks Nat
Got past that part but now a new error
Traceback (most recent call last):
File "/usr/local/phenix-dev-842/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-dev-842/phenix/phenix/refinement/command_line.py", line 96, in run
call_back_handler=call_back_handler)
File "/usr/local/phenix-dev-842/phenix/phenix/refinement/driver.py", line 1376, in run
ncs_manager = self.ncs_manager)
File "/usr/local/phenix-dev-842/phenix/phenix/refinement/strategies.py", line 489, in refinement_machine
fmodels.fmodel_xray().update_f_part(
AttributeError: 'manager' object has no attribute 'update_f_part'
Immediately after bulk solvent modeling and scaling.
F
On Aug 14, 2011, at 5:29 PM, Nathaniel Echols wrote:
> 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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