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to whom it may concern
I am Ladan Mafakher, an Assistant professor at Jundishapur University of Medical Sciences. I would like to use the standalone version of Demo. so I downloaded the Demo package with its dependencies according to the readme file that exists on the Demo website. I have some problems putting dependency files (uniclust30, uniref90, and metaclust). In run_demo2.py these files were located in the local library directory in the Demo package but I could not find any local library in the Demo package. so I created the local library folder in the Demo package and I put all files in this folder(figure1). is that correct? where should I put these files?
Then I started to run the demo according to read me file with the example file that was put in the Demo package but I faced this error"Use the given template to guide the assembly. there is 0 (<2) domain in /media/ravis/data/DEMO/1dquA/1dquA(Figure2 and Figure3). what is the problem and how can I solve it?
I thank you if you help me with this issue.
best regards

Hello Ladan Mafakher,

As the "README.txt" file described, you also should download NR database and multi-domain protein structure library from the DEMO download page. It is correct to create a folder to save all the library, but you should change the corresponding variables in lines 55-59 of "runDEMO.py".

In addition, the correct usage of DEMO is "$pkgdir/run_DEMO2.py protein_name input_dir sequence [Options]", where 'input_dir' is a folder contains dom1.pdb, dom2.pdb. However, the 'input_dir' is missed when you run DEMO, resulting in the program unable to find your query domains in PDB format.

Please let me know if you have other questions.

Thanks,
Xiaogen