PyRosetta Global Docking

[Anonymous]

Dear All,

I am following the PyRosetta tutorial to learn how to preform global docking.

I wrote the following script:

def Global(pose , repeats):

score = list()

for nterm in range(repeats):

pyrosetta.rosetta.protocols.docking.setup_foldtree(pose , 'A_B', Vector1([1]))		#Make chain A ridgid and chain B move

pert_mover = pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover(jump_num , rotation , translation)

pert_mover.apply(pose)



randomize_upstream = pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover(pose , jump_num , pyrosetta.rosetta.protocols.rigid.partner_upstream)

randomize_upstream.apply(pose)



randomize_downstream = pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover(pose , jump_num , pyrosetta.rosetta.protocols.rigid.partner_downstream)

randomize_downstream.apply(pose)



slide = pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact(jump_num)

slide.apply(pose)



movemap = MoveMap()

movemap.set_jump(jump_num , True)

minmover = pyrosetta.rosetta.protocols.simple_moves.MinMover()

minmover.movemap(movemap)

minmover.apply(pose)



score.append(scorefxn(pose))



score.sort()

for value in score:

print(value)

But I get this error:

minmover.apply(pose)

RuntimeError: Caught an unknown exception!

 

 

The strange part is that I sometimes get this error, and sometimes the script works fine. It is a hot or miss.

 

 

 

I tried to ignore this error with try/except, following is my script:

def Global(pose , repeats):

score = list()

for nterm in range(repeats):



try:

pyrosetta.rosetta.protocols.docking.setup_foldtree(pose , 'A_B', Vector1([1]))		#Make chain A ridgid and chain B move

pert_mover = pyrosetta.rosetta.protocols.rigid.RigidBodyPerturbMover(jump_num , rotation , translation)

pert_mover.apply(pose)



randomize_upstream = pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover(pose , jump_num , pyrosetta.rosetta.protocols.rigid.partner_upstream)

randomize_upstream.apply(pose)



randomize_downstream = pyrosetta.rosetta.protocols.rigid.RigidBodyRandomizeMover(pose , jump_num , pyrosetta.rosetta.protocols.rigid.partner_downstream)

randomize_downstream.apply(pose)



slide = pyrosetta.rosetta.protocols.docking.FaDockingSlideIntoContact(jump_num)

slide.apply(pose)



movemap = MoveMap()

movemap.set_jump(jump_num , True)

minmover = pyrosetta.rosetta.protocols.simple_moves.MinMover()

minmover.movemap(movemap)

minmover.apply(pose)



score.append(scorefxn(pose))

except:



score.sort()

for value in score:

print(value)

But I get this different error

ERROR: No structure mods allowed during scoring!

ERROR:: Exit from: /home/benchmark/T/rosetta.Glass/_commits_/main/source/src/core/scoring/Energies.cc line: 748

 

 

 

Anyone can explain to me what I am doing wrong?

[Anonymous]

The `unknown exception!` error was fixed upstream recently. You will need to get a fresh PyRosetta build and re-run your script to see what exactly is wrong. Weekly releases with numbers 150+ should have this issue fixed. Could you please try to upgrading your PyRosetta install and post back results from new version?

Thanks,

[Anonymous]

Also, usually these ‘unknown exception!` is results of a hard failures from which recovery will be problematic so i would advise against trying to catching them.

[Author]

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