- This topic has 6 replies, 2 voices, and was last updated 13 years ago by Anonymous.
December 10, 2010 at 1:35 pm #712Anonymous
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()
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?
December 10, 2010 at 2:53 pm #4720Anonymous
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 #4721Anonymous
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 #4723Anonymous
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 #4724Anonymous
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 #4725Anonymous
Dunno, but it’s very likely. (I’ve never used PyRosetta).
Let us know if it works!
December 10, 2010 at 3:21 pm #4726Anonymous
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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