[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
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://phenix-online.org/mailman/listinfo/phenixbb



More information about the phenixbb mailing list