pdb2vall

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    • July 8, 2013 at 7:11 pm #1640
      Anonymous

        Dear all,

        I am trying to run pdb2vall (a new tool in Rosetta3.5 to create a vall database based on a specific set of pdbs)

        Although all paths are correct, I got this error message:

        pdb2vall.py: getting fasta from pdb_seqres.txt …
        sh: 1: /home/jadabbass/rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/pdb_scripts/get_pdb_new.py: not found
        ERROR:numbering_back_to_pdbseqres(): fails to fetch pdb via get_pdb_new.py
        ERROR: can’t get results from numbering_back_to_pdbseqres().


        Any idea?

        Thank you in advance,

        Jad

      • July 8, 2013 at 11:34 pm #9015
        Anonymous

          It looks like you’re looking for a Rosetta3.5 script in the rosetta3.4 directory. I’d check your paths and environment variables. Are things where they’re supposed to be?

        • July 9, 2013 at 2:32 am #9016
          Anonymous

            Actually, I am still using Rosetta3.4, however, I copied the pdb2vall folder from 3.5. Isn’t supposed to work?

          • July 9, 2013 at 5:39 pm #9020
            Anonymous

              I’m not sure if the pdb2vall scripts will work with 3.4 – they might, but they might also be dependent on Rosetta features which aren’t in 3.4.

              If you still want to try it with 3.4 instead of upgrading to 3.5 fully, I’d take a look at the /home/jadabbass/rosetta3.4/rosetta_tools/fragment_tools/pdb2vall/pdb_scripts/ directory. Check to make sure that all of the files in it got copied over appropriately (especially the get_pdb_new.py script). Also, check the file permissions on the scripts. The executable bit should probably be set on all of the *.py files in that directory.

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