Error when run script “thread_pdb_from_alignment.py”

Member Site › Forums › PyRosetta › PyRosetta – Scripts › Error when run script “thread_pdb_from_alignment.py”

Viewing 3 reply threads
  • Author
    Posts
    • March 9, 2018 at 5:38 pm #2869
      Anonymous

        Hello guys,

        I’m using the ligand docking protocol, and when I put the command below it does not generate the expected output file “2ou0_threaded.pdb”

        command:

        /home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py –template=2anv_A –target=2ou0_ –chain=A –align_format=clustal alignment.aln 2anv_A.pdb 2ou0_threaded.pdbD

        Error:

        Traceback (most recent call last):

          File “/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/scripts/thread_pdb_from_alignment.py”, line 63, in <module>

            template_gaps = alignment.find_gaps(alignment_data,options.template)

          File “/home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/rosettautil/protein/alignment.py”, line 18, in find_gaps

            if sequence == None:

          File “/home/carlos/.local/lib/python2.7/site-packages/Bio/SeqRecord.py”, line 737, in __eq__

            raise NotImplementedError(_NO_SEQRECORD_COMPARISON)

        NotImplementedError: SeqRecord comparison is deliberately not implemented. Explicitly compare the attributes of interest.

        Please, help me?

      • March 9, 2018 at 5:55 pm #14096
        Anonymous

          I think you can try editing /home/carlos/Downloads/Rosetta/rosetta_bin_linux_2017.08.59291_bundle/tools/protein_tools/rosettautil/protein/alignment.py, at line 18 where it has

          if sequence == None:

          change that to

          if sequence is None:

          That will fix the proximal error, though I’m not sure if other errors might pop up.  There are reports that recent updates to Biopython have changed how certain tools behave, which causes many of the scripts in Rosetta which use it to break. You may or may not run into that issue.

        • March 9, 2018 at 7:30 pm #14097
          Anonymous

            I did not find the part “if sequence == None:”

            But I found at least 3 regions with “find_gaps”

            I still do not know what to do.

             

            My script printscreen

            https://uploaddeimagens.com.br/imagens/captura_de_tela_de_2018-03-09_16-28-58-png

            • March 12, 2018 at 8:59 pm #14109
              Anonymous

                The “if sequence == None:” is not in the thread_pdb_from_alignment.py script itself, it’s in a script that the thread_pdb_from_alignment.py script is calling. (alignment.py in tools/protein_tools/rosettautil/protein/)

            • March 13, 2018 at 2:12 pm #14115
              Anonymous

                Thank you rmoretti

                It worked after the modification.

                Sorted out.

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