[phenixbb] SA-torsion refinement

esmael haddadian at uchicago.edu
Wed Sep 9 12:40:49 PDT 2009

Hi Ralf,

Thanks a lot for the info.  I downloaded the latest phenix version for  
MAC; we I ran it I got this error message.

toshow_stack(1): /usr/local/phenix-1.4-159/cctbx_project/cctbx/sgtbx/ 
__init__.py(79) __init__
show_stack(2): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ 
__init__.py(181) space_group_info
show_stack(3): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ 
__init__.py(677) crystal_symmetry
show_stack(4): /usr/local/phenix-1.4-159/cctbx_project/iotbx/mtz/ 
crystal_symmetry_from_mtz.py(9) extract_from
show_stack(5): /usr/local/phenix-1.4-159/cctbx_project/iotbx/ 
crystal_symmetry_from_any.py(73) extract_from
show_stack(6): /usr/local/phenix-1.4-159/cctbx_project/iotbx/ 
crystal_symmetry_from_any.py(87) extract_and_append
show_stack(7): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ 
command_line.py(462) process_args
show_stack(8): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ 
command_line.py(208) __init__
show_stack(9): /usr/local/phenix-1.4-159/phenix/phenix/refinement/ 
command_line.py(68) run
show_stack(10): /usr/local/phenix-1.4-159/phenix/phenix/command_line/ 
refine.py(11) <module>
Bus error (Python call stack above)
                 This crash may be due to a problem in any imported
                 Python module, including modules which are not part
                 of the cctbx project. To disable the traps leading
                 to this message, define these environment variables
                 (e.g. assign the value 1):
                 This will NOT solve the problem, just mask it, but
                 may allow you to proceed in case it is not critical.

Defining the variables did not help.  Could you please advise.


On Sep 8, 2009, at 4:02 PM, Ralf W. Grosse-Kunstleve wrote:

>> Does phenix have SA-torsion angle refinement option similar to what  
>> is
>> available in CNS?
> Yes, with a recent installer (less than a week or two old) you can try
> it out by adding
>        simulated_annealing_torsion=True
> in addition to the other settings for turning on simulated annealing.
> There are some known problems that I didn't have a chance to fix yet,
> but if it doesn't crash it should be OK. If you get a crash or weird
> results, let me know.
> Ralf
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb

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