Fold tree not correct for multi-chain partners

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- December 10, 2010 at 1:35 pm #712
  Anonymous
  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()
  dock_prot.setup_foldtree(p,’ABCD_X’)
  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:
  
  p.pdb_info().pdb2pose(‘X’,1)
  
  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?
- December 10, 2010 at 2:53 pm #4720
  Anonymous
  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…?
- December 10, 2010 at 2:57 pm #4721
  Anonymous
  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.
- December 10, 2010 at 2:59 pm #4723
  Anonymous
  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.
- December 10, 2010 at 3:02 pm #4724
  Anonymous
  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, #3A translation, 8 degrees rotation
  spin = RigidBodySpinMover( dock_jump )
  slide_into_contact = DockingSlideIntoContact(dock_jump)
- December 10, 2010 at 3:07 pm #4725
  Anonymous
  Dunno, but it’s very likely. (I’ve never used PyRosetta).
  
  Let us know if it works!
- December 10, 2010 at 3:21 pm #4726
  Anonymous
  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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