Foldtree setup, jump problem in PyRosetta 2.0

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    • July 21, 2011 at 7:00 pm #988
      Anonymous

        For some reason, PyRosetta is only identifying two jumps in my Pose, where in version 1.0 I had three. Using jump=3 with the following gives me an error when I try to randomize or dock.

        Here is my chain layout: AB_X

        Here are the foldree commands I am issuing:


        jumpVec = rosetta.Vector1([3])
        rosetta.protocols.docking.DockingProtocol.setup_foldtree(pose,'AB_X',jumpVec)
        print pose.fold_tree()
        print str(pose.num_jump())+" jumps."

        which prints:


        FOLD_TREE EDGE 1 371 -1 EDGE 371 743 1 EDGE 743 752 -1 EDGE 743 738 -1 EDGE 371 735 -1 EDGE 735 736 2 EDGE 736 737 -1
        2 jumps.

        PDB File:


        ...
        ...
        ATOM 11565 HN GLY A 735 ...
        ATOM 11566 CA GLY A 735 ...
        ATOM 11567 1HA GLY A 735 ...
        ATOM 11568 2HA GLY A 735 ...
        TER
        HETATM11569 CA CA B 1 ...
        HETATM11570 CA CA B 2 ...
        TER
        ATOM 11571 N ASP X 1 ...
        ATOM 11572 1H ASP X 1 ...
        ATOM 11573 2H ASP X 1 ...
        ATOM 11574 3H ASP X 1 ...
        ATOM 11575 CA ASP X 1 ...
        ...
        ...

      • July 21, 2011 at 7:10 pm #5897
        Anonymous

          If those are calcium atoms, you should have 3 jumps total: A to X, A to calcium 1, A to calcium 2. Probably some intervening code has changed and is no longer properly assigning a jump; probably the two calciums are connected improperly by bond; I’m guessing that’s what is going on with edge EDGE 736 737 -1.

          I don’t know how to trace where code in the middle has changed between PyRosetta versions, so let’s look at some of the other options?

          A) If the CA atoms are not at your interface, just delete them, and add them back in later.
          B) It appears the between-proteins jump is now numbered 1; try setting your movers to work on jump number 1.
          C) If neither of those work, we can try repairing the fold tree. I think it can be repaired by deleting EDGE 736 737 -1 and replacing it with an EDGE 735 737 2. (So long as the protein-to-CA jumps aren’t flexible, it doesn’t really matter where in protein 1 they originate). (Also, I don’t mean literally editing the string here, I mean modifying the FoldTree. I think there may be a text-based FoldTree read in method though). If that’s too vague I can describe it in C++ better.

        • July 22, 2011 at 3:25 pm #5900
          Anonymous

            Okay, the jump=1 seems to be working. Thanks.

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