Hello!
I am trying to run the default XML script to change the specificity of a protein so that it binds to a DNA sequence of interest. For this I am referring to the book Redesigning the specificity of protein-DNA interactions with Rosetta
Thyme S, Baker D. Redesigning the specificity of protein-DNA interactions with Rosetta. Methods Mol Biol. 2014;1123:265-82. doi: 10.1007/978-1-62703-968-0_17. PMID: 24510272.
However I am getting the following error message.
File: src/protocols/rosetta_scripts/RosettaScriptsParser.cc:1199
Input rosetta scripts XML file "scriptfile.xml" failed to validate against the rosetta scripts schema. Use the option -parser::output_schema <output filename> to output the schema to a file to see all valid options.
Your XML has failed validation.
Can you please tell me how i can use rewrite_rosetta_script.py to update my XML script file?
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You should be able to call
(substitue path as appropriate).
Note the script is a little on the older side, so it's currently written for Python 2 -- it won't (currently) work with Python 3, though that's now on my list to fix.
Thank you! I tried it and it worked!