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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