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
