[phenixbb] twin refinement error

Imre Törő toro at embl.de
Wed Apr 8 08:32:56 PDT 2009


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.
>>
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>>   
>>     
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