[phenixbb] twin refinement error

jonathan elegheert jonathan.elegheert at ugent.be
Wed Apr 8 08:47:49 PDT 2009


Hi Pavel,

the error indeed disappeared but was unfortunately replace with another 
one; it seems to involve the function _rna_sugar_pucker_analysis, but I 
have only protein in my input.

Jonathan

-------------------------------------

Traceback (most recent call last):
  File "/usr/local/phenix-1.4-30/phenix/phenix/command_line/refine.py", 
line 19, in <module>
    command_line.run(command_name="phenix.refine", args=sys.argv[1:])
  File 
"/usr/local/phenix-1.4-30/phenix/phenix/refinement/command_line.py", 
line 68, in run
    log=log)
  File 
"/usr/local/phenix-1.4-30/phenix/phenix/refinement/command_line.py", 
line 227, in __init__
    self.pdb_file_names)
  File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/utils.py", line 
833, in process_pdb_files
    raw_records    = raw_records)
  File "/usr/local/phenix-1.4-30/cctbx_project/mmtbx/utils.py", line 
864, in _process_pdb_file
    log                      = self.log)
  File 
"/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2881, in __init__
    log=log)
  File 
"/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 2029, in __init__
    log=log)
  File 
"/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 1507, in __init__
    prev_mm=prev_mm)
  File 
"/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 504, in __init__
    prev_mm=prev_mm)
  File 
"/usr/local/phenix-1.4-30/cctbx_project/mmtbx/monomer_library/pdb_interpretation.py", 
line 534, in _rna_sugar_pucker_analysis
    raise RuntimeError("Feature disabled because of known problems.")
RuntimeError: Feature disabled because of known problems.


Imre Törő wrote:
> Dear Pavel,
>
> One of my structure suffers exactly from the same PM twinning 
> (b=sqrt(3)*a, gamma=119.8, C222(1)==>P6(3)22), but this involves then 
> three twinned domains. Is it possible to specify both operators in 
> phenix.refine, and if yes, how?
>
> Thankx in advance,
>
> Imre
>
> Pavel Afonine írta:
>   
>> Hi Jonathan,
>>
>> this is a bug and it is fixed already. Please use one of the latest 
>> development versions of PHENIX:
>>
>> https://www.phenix-online.org/download/phenix/nightly/
>>
>> Pavel.
>>
>>
>> On 4/8/09 8:02 AM, jonathan elegheert wrote:
>>   
>>     
>>> Dear Phenix developers,
>>>
>>> I am rigid-body refining a PM-twinned structure (C2221 => P6x22) with 
>>> the operators suggested from xtriage or SFcheck but I keep running into 
>>> this same error (version 1.4.3 or latest cci aps bundles);
>>>
>>> 1/2*h-1/2*k,-3/2*h-1/2*k,-l
>>> 1/2*h+1/2*k,3/2*h-1/2*k,-l
>>>
>>> Any suggestions as to how I can resolve this?
>>>
>>> Many thanks in advance,
>>>
>>> Jonathan Elegheert
>>> PhD student
>>> Ghent University
>>> Belgium
>>>
>>> -------------------------------------------------------------------------
>>>
>>> Traceback (most recent call last):
>>>   File 
>>> "/usr/local/cciapps/cci_apps_sources/phenix/phenix/command_line/refine.py", 
>>> line 16, in <module>
>>>     command_line.run(command_name="phenix.refine", args=sys.argv[1:])
>>>   File 
>>> "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/command_line.py", 
>>> line 89, in run
>>>     call_back_after_monitor_collect=call_back_after_monitor_collect)
>>>   File 
>>> "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/driver.py", 
>>> line 1121, in run
>>>     call_back_after_monitor_collect = call_back_after_monitor_collect)
>>>   File 
>>> "/usr/local/cciapps/cci_apps_sources/phenix/phenix/refinement/strategies.py", 
>>> line 190, in refinement_machine
>>>     twin_law = sgtbx.rt_mx( params.twinning.twin_law )
>>> RuntimeError: cctbx InternalError: 
>>> /net/garter/scratch1/rwgk/auto_build/sources/cctbx/sgtbx/rt_mx.cpp(230): 
>>> Unsuitable value for rational rotation matrix.
>>>
>>> _______________________________________________
>>> phenixbb mailing list
>>> phenixbb at phenix-online.org
>>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>>   
>>>     
>>>       
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