Symmetric pose initialization fails

Member Site Forums PyRosetta PyRosetta – General Symmetric pose initialization fails

Viewing 3 reply threads
  • Author
    • #1767

        Hi all.

        I am using PyRosetta for Windows, and after running the following code sample:

        pose = pose_from_sequence("AAAAAAAAAAAAA", "fa_standard")
        pose_symm_data = core.conformation.symmetry.SymmData(pose.n_residue(),pose.num_jump())
        core.pose.symmetry.make_symmetric_pose(pose, pose_symm_data)

        it fails with an error:
        “core/pose/PDBInfo.hh PDBInfo::natoms( Size const res): res is not in this PDBInfo!”

        The assert is coming from PDBInfo.hh, line 363:

        "PyAssert( (res>0) && (res < residue_rec_.size()), "PDBInfo::natoms( Size const res): res is not in this PDBInfo!" );"

        Where as I understand it should say res <= residue_rec_.size(). Is this assumption correct? And is there a way I can recompile PyRosetta for Windows with these changes? Thank you! PS:
        As a workaround I modified the binary rosetta.dll directly, effectively disabling the assert checks:
        “Comparing files rosetta.dll and rosetta_bak.dll
        0058A2ED: 90 76
        0058A2EE: 90 1B
        0058A308: EB 72

      • #9526

          Looks like you’re right. I’ll fix it in the developer’s version, and it should be fixed for the next PyRosetta release.

          Thanks for the bug report!

        • #9527

            Since the windows version of PyRosetta is no longer supported or updated, you will have to download the next weekly release of the Rosetta trunk and compile PyRosetta from that. I’m not sure what compilation tools are available outside of the development version of the rosetta source, or windows-specific tricks to compile, so I am contacting Sergey Lyskov to get his thoughts on the compile. There is still a lot of interest in the windows version, so I’m not sure why it is not supported any longer.


          • #9528

              Compilation process for Windows version is a bit complicated. Basically you need to generate bindings sources on Linux or Mac then transfer results to Windows box and compile it with VisualStudio. This is laborious process so I would advise against trying it on your own.

          Viewing 3 reply threads
          • You must be logged in to reply to this topic.