How to convert fragments to PDB format?

Member Site Forums Rosetta 3 Rosetta 3 – General How to convert fragments to PDB format?

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    • #2261

        Dear Sir/Madam,

        I was wondering if there is a tool inside Rosetta that lets me convert a fragment (9-mer for instance) taken from the fragment file of 9-mers into a PDB-like format file.
        Any suggestions/information?

        Thank you,

      • #11178

          Unfortunately, there isn’t a good way to easily go from a fragments file to PDB format. There is a way to tell the fragment picker to output a silent file instead of a fragments file (-frags::output_silent), but nothing which will convert the fragments file.

          You may have to write a script to do this for you. (PyRosetta may be helpful here). I see two options. Either you can read the phi/psi angles from the fragment file and set them in a peptide, or you can read off the source information encoded in the fragment file, and just grab that region from the original PDBs.

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