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How to use rewrite_rosetta_script.py to update XML script file?

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How to use rewrite_rosetta_script.py to update XML script file?
#1
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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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Fri, 2024-03-15 06:44
intomybioverse
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You should be able to call 

python2 path/to/Rosetta_main/tools/xsd_xrw/rewrite_rosetta_script.py --input scriptfile.xml --output scriptfile_new.xml

(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.

Fri, 2024-03-15 06:54
rmoretti
(Reply to #3)
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Thank you! I tried it and it worked!

Sun, 2024-03-17 06:22
intomybioverse