obtaing pdb files

Member Site Forums Rosetta 3 Rosetta 3 – General obtaing pdb files

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    • #805


        I have read about a python script used in Meiler lab does which clean and fix obvious errors in pdb. However I have been unable to locate in the rosseta 3.2 package. is this script public available.

        Knut J

      • #5082

          Hi Knut,

          The Meiler lab uses a cleaning script that was created by:

          1. Phil Bradley
          2. Rhiju Das
          3. Michael Tyka
          4. TJ Brunette
          5. James Thompson

          The script was modified to work with the Meiler lab configuration. James Thompson has included the cleaning script in the Rosetta 3.2 release. You can find the script in your rosetta_source directory: rosetta-3.2/rosetta_source/src/python/apps/public/get_pdb.py

          In general, you run it by: python get_pdb.py

        • #5084

            Thank. I have also made a modification which is very simple. I have adde my modification below. I think it simple to give a clear error message rather than just fail. How can I provide a patch?

            pdbname = argv[1]
            pdbcode = argv[1]
            chainid = argv[2]
            print “please provide the name of the pdb file, the pdb code and chain id”
            print “”
            assert( len(argv)>2)

          • #5098

              Hi Knut,

              I will make those changes to the script. Soon, the version that the meiler lab uses will be available online.

              Steven C.

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