how to generate Fragments using up to 2001 structures only

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    • July 25, 2015 at 7:43 am #2238
      Anonymous

        Hello!

        I am trying to replicate an old experiment and I’d need to generate fragments using old structures only. How can I do that?
        at the moment I created a database of old structures and I downloaded the rosetta fragment picker tool so I am trying to find out what internal database of rosetta I should update, any suggestions?

        Thanks a lot in advance

      • August 6, 2015 at 3:57 pm #11113
        Anonymous

          The fragment picker works off of the “Vall” database of filtered structure input. To limit the fragments to certain structures, you just need to generate (or obtain) a Vall which corresponds to the limited set of PDBs. In Rosetta/tools/fragment_tools/pdb2vall/ there is a script which should be able to generate a Vall database from a set of PDB files.

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