of Rosetta VS cleanATOM of PyRosetta

Member Site Forums Rosetta 3 Rosetta 3 – Applications of Rosetta VS cleanATOM of PyRosetta

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    • #2006

        Dear friends,
        I am dealing with a PDB file missing some residues. I think I should clean it by of Rosetta or cleanATOM of PyRosetta.

        In Rosetta, the clean_pdb ignores the missing positions and renumber all the residues from 1 to the end regardless of the missing gap.

        In PyRosetta, the missing gap can still be remained.

        Can I ask can I get the result similar to cleanATOM by using Rosetta’s I think I should clean the PDB first, then do loop modeling for the missing residues. Is that correct?

        Thank you very much.

        Yours sincerely

      • #10317

          I don’t think there’s an option in the distributed clean_pdb script not to renumber the residues.

          Now-a-days, though, Rosetta itself is pretty good at cleaning up PDBs if you pass the appropriate options. I myself tend to use Rosetta directly, rather than relying on an external script. Try something like the following commandline:

          main/source/bin/score_jd2.linuxgccrelease -ignore_unrecognized_res -ignore_zero_occupancy false -out:pdb -s FILE_TO_CLEAN.pdb

          This hopefully will result in a FILE_TO_CLEAN_0001.pdb file which represents what Rosetta thinks the PDB looks like.

          Sometimes it doesn’t quite work, but usually in those cases it’s a quick fix with a search/replace or deleting lines with a text editor.

          (Edit: fixed commandline)

        • #10322

            (I do not know why but it seems that recently I always encountered error when I submit a comment in this forum. It turned out to be okay when I re-edit the comment)

            Hi R Moretti,
            It really works, so amazing!

            A new file of file_0001.pdb (and was created, 1) with full hydrogens, 2) without filling the missing residues to re-number, 3) with score comment in the end

            So I delete the score in the end to get a clean PDB file.

            Thank you very much.

            (The first trial did generate any file though the prompt in the terminal seemed to be okay. So I tried again and got those files. But anyway, the problem has been solved.)

            (Just to correct, it is score_jd2 instead of sdore_jd2) :)

            Yours sincerely

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