clean_pdb not working

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    • July 23, 2020 at 11:48 am #3514
      Anonymous

        The simple clean_pdb.py does not function.

        When I look at the script it is trying to print the wget_cmd command, WHY??

        Here is the input and output:

        python /home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py 2n2a AB

          File “/home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py”, line 56

            print wget_cmd

                  ^

        SyntaxError: Missing parentheses in call to ‘print’. Did you mean print(wget_cmd)?

        What is wrong here?

         

      • July 27, 2020 at 5:47 pm #15420
        Anonymous

          Many of the scripts in Rosetta are written for Python2. As such, they won’t necessarily work for Python3.  (We’re slowly transitioning things to Python3, but depending on which version of Rosetta you use and which scripts you use, they might be Python2 specific.)

          The error you’re getting is the result of trying to run a script written for Python2 only on a Python3 interpreter. Try explicitly invoking Python2 by providing the version number for the python interpreter.

          python2.7 /home/aserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py 2n2a AB

        • July 28, 2020 at 5:17 am #15421
          Anonymous

            Thank yopu for the reply, I have checked the python version, it is python 2, here is the output:

            Infinity1s-iMac:TOMs andreserobian$ python –version

            Python 2.7.16

             

            Ok, so I tried explicitly calling python 2.7 and this is the input and output:

            python2.7 /Users/andreserobian/Documents/rosetta/tools/protein_tools/scripts/clean_pdb.py ae-pep1 A

            Found existing PDB file at ae-pep1.pdb

            ae-pep1 A     0 — — — — BAD

             

            Why is it saying BAD?

             

            • July 28, 2020 at 3:24 pm #15422
              Anonymous

                That shows up if there are no valid residues which the script can find in the PDB.

                If the PDB is otherwise properly formatted (e.g. if you can open it with PyMol or Chimera or the like), the most common reason for that is having all atoms be zero occupancy. One of the tasks of the clean_pdb script is to remove the zero occupancy atoms. If a residue is missing or has zero occupancy for critical backbone atoms (N, CA, C), then the whole residue is discarded.

                There isn’t a setting to change the script’s behavior in this — you’d need to manually change the occupancy column in the PDB.

                 

                Alternatively, you can try simply skipping the clean_pdb step. This script was much more critical in the past. Over the years Rosetta has been made much more robust to various PDB input, and can handle inputs which it would previously choke on.

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