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 [email protected] 2009/1/28 Jesse Sundlov <[email protected]>: > 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 >
