[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
>>>
>>>
>>>
>> _______________________________________________
>> phenixbb mailing list
>> phenixbb at phenix-online.org
>> http://www.phenix-online.org/mailman/listinfo/phenixbb
>>
>>
> _______________________________________________
> phenixbb mailing list
> phenixbb at phenix-online.org
> http://www.phenix-online.org/mailman/listinfo/phenixbb
>
More information about the phenixbb
mailing list