Sorry for a typo, it should be
Dear Jesse,
It looks that both processes had problems when BALBES tried to get
template MR models. Could you please provide us with the log files
under the subdirectories 'process_details/' so that we can take a look
to find out what happened.
Thanks
Fei
2009/1/28 Dr. F Long <[log in to unmask]>:
> Dear Jesse,
>
> It looks that both progress had problems when BALBES tried to get
> template MR models. Could you please provide us with the log files
> under the subdirectories 'process_details/' so that we can take a look
> to find out what happened.
>
> Thanks
>
> Fei
>
> Dr Fei Long
> YSBL
> University of York
> [log in to unmask]
>
>
>
>
> 2009/1/28 Jesse Sundlov <[log in to unmask]>:
>> Hello All,
>>
>> I'm trying to use BALBES locally to perform molecular replacement on data of
>> a two protein complex.
>>
>> Protein 1 is a truncated version of a two domain protein of known
>> structure.
>> Protein 2 has a homologous protein of known structure and ~50% identity.
>>
>> I'm having two related problems -
>>
>> 1> If I include the truncated PDB of Protein 1 as an input model, along with
>> a .seq file containing the two sequences, I get the following error:
>>
>>
>>
>> #-----------------------------------------------------------#
>> # Search for Structures with Similar Cell and Space Group #
>> #-----------------------------------------------------------#
>> No structure of similar cell and space group was found
>>
>> #-----------------------------------------------------------#
>> # Model Database Analysis #
>> #-----------------------------------------------------------#
>> number of amino acids in the input sequence file is 615
>> 1 structures found to be above 20% identity with the given sequence,
>> of which the best identity is 100.0
>> Error message : no structure was found
>> *------------------------------------------------------------------------------------*
>> | All of search model PDB files are
>> in: |
>> | Subdirectory:
>> template_models |
>> *------------------------------------------------------------------------------------*
>> BALBES exits after searching the internal database
>>
>>
>>
>>
>> 2> If I repeat this, but use a .seq file that has the two sequences merged
>> as one, I get this error:
>>
>>
>>
>> #-----------------------------------------------------------#
>> # Search for Structures with Similar Cell and Space Group #
>> #-----------------------------------------------------------#
>> No structure of similar cell and space group was found
>>
>> #-----------------------------------------------------------#
>> # Model Database Analysis #
>> #-----------------------------------------------------------#
>> number of amino acids in the input sequence file is 615
>> 2 structures found to be above 20% identity with the given sequence,
>> of which the best identity is 100.0
>> can not create a reader object for XML file for
>> /Users/B/Test/xml/get_structure_DB_Protein1.xml
>> Traceback (most recent call last):
>> File "/apps/ccp4-6.1.0/bin/balbes", line 154, in <module>
>> sfAnalysisIni.Sfcheck.info_strucFactor.get_b_overall())
>> File "/apps/BALBES_0.0.1/bin_py/exeCodeClasses.py", line 532, in execute
>> self.SearchDB.controller()
>> File "/apps/BALBES_0.0.1/bin_py/exeCodeClasses.py", line 1378, in
>> controller
>> self.structDB_info_analysis()
>> File "/apps/BALBES_0.0.1/bin_py/exeCodeClasses.py", line 881, in
>> structDB_info_analysis
>> rootElement = StripXml(struct_xml_document.documentElement)
>> UnboundLocalError: local variable 'struct_xml_document' referenced before
>> assignment
>>
>>
>> Ideas? Any help would be greatly appreciated
>>
>> -Jesse
>>
>
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