Syntax to extract PDB files from a silent file

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    • September 26, 2014 at 8:48 pm #2009
      Anonymous

        Dear friends,
        I think there is nothing incorrect in my command line to extract PDB files from a silent file:

        ~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:silent /mnt/hgfs/Downloads/silent.out -in:file:fullatom -in:file:silent_optH -out:output

        The prompt goes well and completes successfully:

        …
        core.pack.dunbrack: Dunbrack 2010 library took 0.480358 seconds to load from binary
        protocols.jd2.JobDistributor: protein_0001_0001 reported success in 3 seconds
        protocols.jd2.JobDistributor: no more batches to process…
        protocols.jd2.JobDistributor: 1 jobs considered, 1 jobs attempted in 3 seconds

        However, there is no any PDB files in /mnt/hgfs/Downloads. Only a file of score.sc is created.

        It still remains the same though “-out:path:all -out:path:all” is added.

        Can I ask how to get the PDB file?

        Thank you very much.

        Yours sincerely
        Cheng

      • September 26, 2014 at 9:54 pm #10336
        Anonymous

          After referring to
          https://www.rosettacommons.org/node/3814

          I know the answer now:

          Just change “-out:output” into “-out:pdb”. :)

          Cheng

          ~/Cheng/rosetta_2014.30.57114_bundle/main/source/bin/score_jd2.linuxgccrelease -database ~/Cheng/rosetta_2014.30.57114_bundle/main/database -in:file:silent /mnt/hgfs/Downloads/silent1.out -in:file:fullatom -in:file:silent_optH -out:pdb

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