Can only relax one structure at a time

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    • December 12, 2012 at 9:55 am #1485
      Anonymous

        I have never been able to give the relax application more than one structure at a time, but now I have hundreds and doing each individually just isn’t an option. How can I do this?

        my flags file contains:
        -in:file:l inputs

        the inputs file contains:
        00_wildtype_0016_0001.pdb
        00_wildtype_0016_0002.pdb
        ...
        00_wildtype_0016_0203.pdb

        all the input files are in the current directory.

        The error is:
        protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0201.pdb nstruct index 1
        protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0202.pdb nstruct index 1
        protocols.jd2.PDBJobInputter: pushing 00_wildtype_0016_0203.pdb nstruct index 1
        core.io.pdb.file_data: Adding undetected upper terminus type! 146
        core.pack.task: Packer task: initialize from command line()
        protocols.evaluation.ChiWellRmsdEvaluatorCreator: Evaluation Creator active ...
        protocols.jd2.PDBJobInputter: PDBJobInputter::pose_from_job
        core.import_pose.import_pose: PDB File:00_wildtype_0016_0001.pdb not found!

        Note that if I specify a single structure in the flags file:
        -in:file:s 00_wildtype_0016_0001.pdb

        It works just fine.

        How is it possible to give Rosetta a list of structures to work on?

      • December 12, 2012 at 2:49 pm #8226
        Anonymous

          This ought to work fine, assuming that 00_wildtype_0016_0001.pdb is in the directory in which you are running Rosetta (which it would have to be for -s 00_wildtype_0016_0001.pdb to work without a path).

          Post your -l file. My best guess is there is some sort of nonprinting character at the end of the line in your -l file. Are you using any path options in your options file?

        • December 12, 2012 at 7:06 pm #8228
          Anonymous

            The non-printing charachter is my guess too. That would be especially likely if you prepared the list with a Windows machine (which ends lines with a ‘rn’ combo) and were reading it on a Linux or MacOS 10 machine (which end lines with just ‘n’). The “extra” ‘r’ may be confusing things.

          • December 14, 2012 at 9:40 pm #8236
            Anonymous

              “How do I convert between Unix and Windows text files?”

              http://kb.iu.edu/data/acux.html

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