Fold tree not correct for multi-chain partners

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    • #712

        I have a two partner docking problem, where the first partner is made up of chains A,B,C,and D, and the second partner is chain X. They are loaded from a single PDB.

        In my script I am using:

        dock_prot = DockingProtocol()
        print p.fold_tree()

        Which prints:

        FOLD_TREE EDGE 1 117 -1 EDGE 117 118 1 EDGE 118 227 -1 EDGE 227 235 -1 EDGE 227 479 4 EDGE 235 236 2 EDGE 236 353 -1 EDGE 353 354 3 EDGE 354 471 -1 EDGE 479 472 -1 EDGE 479 486 -1

        However, once the pose is created, a command such as:


        will work and returns the correct AA #. I tried creating my own fold tree, but received an error. Is my docking protocol fold tree sytax correct?

      • #4720

          The fold tree appears to be correct. I think your confusion is caused by the fact that the fold tree reports residue numbers, not PDB numbering. (Internally, Rosetta counts residues from 1 at all times; PDB info is maintained in a separate data structure).

          Is it not working…?

        • #4721

            The output is showing a jump at EDGE 117 118 1, but I have explicitly set it with dock_prot.setup_foldtree(p,’ABCD_X’). So the jump should be further down. Right now the docking is doing A_BCDX.

          • #4723

              You have 4 chains, thus you have 4 jumps (A to B, B to C, C to D, and somebody to X). The issue then is telling it which jump is the MOBILE jump – in your case, 4.

            • #4724

                So this would be done with the dock_jump parameter?

                #initial perturbation movers
                randomize1 = RigidBodyRandomizeMover(p, dock_jump, partner_upstream)
                randomize2 = RigidBodyRandomizeMover(p, dock_jump, partner_downstream)
                dock_pert = RigidBodyPerturbMover(dock_jump, 3, 8) #3A translation, 8 degrees rotation
                spin = RigidBodySpinMover( dock_jump )
                slide_into_contact = DockingSlideIntoContact(dock_jump)

              • #4725

                  Dunno, but it’s very likely. (I’ve never used PyRosetta).

                  Let us know if it works!

                • #4726

                    Yup, that worked!

                    I needed to specify “dock_prot.setup_foldtree(p,’ABCD_X’)” and then set dock_jump equal to 4.

                    Thanks for the help.

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