How to combine two chains

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    • July 19, 2016 at 2:54 pm #2471
      Anonymous

        I just seperately modeled two halves of an IgG1 Fc as two seperate pdb’s and I need to combine them into one.  How would I be able to do that?  Or just in general how would I be able to combine two  pdb’s into one?

      • July 19, 2016 at 3:26 pm #11746
        Anonymous

          The easy way is with a text editor (emacs, vi, atom).

           

          Within pyrosetta, there’s a pose utility function append_pose_to_pose that should do it.

        • July 19, 2016 at 6:40 pm #11749
          Anonymous

            How exactly do I modify a text file to include both pdb’s?  Also I’m not trying to model the docking.  I wasn’t able to model the whole antibody Fc because the template was made of two chains, so Swiss-Model didn’t allow for that.  Because of that, I had to model each half seperately and now I just want to put the two halves together.  When I open the two pdb’s in PyMol everything appears correct, I just don’t know how to save it as one pdb.

          • July 19, 2016 at 3:31 pm #11748
            Anonymous

              Um, considering your question further, I’m talking about the literal act of merging two poses.  You may be talking about the more scientific question of “I have two things that bind, how do I model their binding”? 

              For two halves of an antibody, I would align the two parts to a homologous antibody (in pymol or whatever), then do either relax or refinement-only docking.  (I’m not a pyrosetta person, but those two tools are available from the command line version, probably they’re in pyrosetta too).

              For a less well known problem than two halves of an antibody, docking is the tool you’d want.

            • July 19, 2016 at 7:34 pm #11751
              Anonymous

                PDBs are human-readable text files, you can just open them up in emacs or notepad or whatever and look at them.  If you are on windows, open both PDBs in notepad and literally just cut-and-paste them together into one file.  If you’re on mac, it’s probably called textedit; if linux, gedit is simplest for new users.

                Assuming the two files have separate chain letters, and you don’t care about any of the non-coordinate lines, and you’re not on windows, from command line:

                cat pdb1 | grep ATOM > combined.pdb

                cat pdb2 | grep ATOM >> combined.pdb

                now combined.pdb is all the ATOM records of both files.

                 

              • July 22, 2016 at 1:53 pm #11753
                Anonymous

                  I was able to do it, thank you so much.

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