Help with get_pdb.py for PDB file cleaning

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  • This topic has 7 replies, 5 voices, and was last updated 13 years ago by Anonymous.
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    • March 28, 2011 at 9:11 am #844
      Anonymous

        Hi, I am following the suggestion from one of the posts here to use get_pdb.py to clean up my PDB files. However, I always got the error message:

        Traceback (most recent call last):
        File “/usr/local/rosetta3.2/rosetta_source/src/python/apps/public/get_pdb.py”, line 69, in ?
        assert( len(argv)>2)
        AssertionError

        Did I do something incorrectly? Thanks in advance for any kind help!

      • March 28, 2011 at 3:06 pm #5245
        Anonymous

          I know nothing about get_pdb.py specifically.

          Speaking from knowledge of python, the error “len(argv)>2” implies that the code expects to have no greater than two arguments. How many arguments are you giving it…?

        • March 30, 2011 at 9:03 am #5264
          Anonymous

            It’s working now with the option -ignorechain and with fresh pdb files downloaded from PDB. Interestingly, it still does not work on my old pdb files, which have been slightly modified by me previously. Thank you very much for the help!!

          • March 30, 2011 at 3:37 pm #5272
            Anonymous

              Hi lzx32,

              For some reason, the clean_pdb.py script from the Meiler lab has some peculiarities. For instance, if the protein has been already clean, or is a state that it can not be cleaned, the script will crash out.

              Steven C.

            • March 28, 2011 at 3:27 pm #5248
              Anonymous

                … actually, it’s the other way around. “assert( len(argv)>2)” is the line which is raising the AssertionError, and the assertion error is raised because the thing passed to assert is false. That is, len(argv) is not greater than two – the code expect to have two or more command line parameters (one of the entries in argv is the script name).

                Specifically, it looks like the script expects the first command line parameter to be the pdb name, and the second to be the chain ID. Parameters 3 and up can include ‘-nopdbout’, ‘-nochain’ and ‘-ignorechain’ (it looks like anything else is ignored). Flags have to be at position 3+; putting the option flags before the pdb name and chain ID will not work.

              • March 28, 2011 at 3:38 pm #5251
                Anonymous

                  greater than, less than…it’s too early in the week for that.

                • December 2, 2011 at 1:44 am #6355
                  Anonymous

                    I am unable to locate the clean_pdb.py file in my rosetta_source directory, currently I am using rosetta 3.3. Please tell me where I woud find the same file for cleaning my structures?

                  • December 8, 2011 at 4:11 pm #6376
                    Anonymous

                      http://www.meilerlab.org/jobs/downloadfile/name/scripts.tgz

                      http://www.meilerlab.org/index.php/jobs/resources ; rosetta tab

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