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Different results FastRelax pyrosetta vs rosetta_scripts

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Different results FastRelax pyrosetta vs rosetta_scripts
#1
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Hi everyone,

I want to relax a designed disulfide bond with FastRelax, but when I try to do it in Pyrosetta it seems like it gets no optimization at all. However, when I try FastRelax in rosetta scripts I get a good geometry. Could you please help me identify what I am missing in my Pyrosetta code?

Thank you! 

## Pyrosetta
fast_relax = protocols.relax.FastRelax(scorefxn_in=scorefxn, standard_repeats=5)
movemapOptions = core.kinematics.MoveMap()
movemapOptions.set_chi(True); movemapOptions.set_bb(True); movemapOptions.set_jump(True)
fast_relax.set_movemap(movemapOptions)
fast_relax.set_task_factory(taskOper)
fast_relax.apply(pose)
pose.dump_pdb("test.pdb")


## Rosetta_script
<MOVERS>
 <FastRelax name="relax" scorefxn="ref2015" task_operations="init,repackonly,norepack" repeats="5">
    <MoveMap name="moveMap" bb="1" chi="1" jump="1"/>
 </FastRelax>
</MOVERS>

 

Category: 
PyRosetta
Post Situation: 
Unsolved
Tue, 2023-06-20 09:52
karenjgonzalez
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Hi!

When you set the task_factory... what are the operations that you have set in the taskOper? You didn't include those in the pyrosetta example

Wed, 2023-08-09 05:01
diegoms
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Hi,

Thank you for your reply. Below are the task operations 

### Neighbors 12 Angs around disulfide forming residues
disulf_res1 = 98
disulf_res2 = 124
focus_selector = core.select.residue_selector.ResidueIndexSelector(disulf_res1)
focus_selector.append_index(disulf_res2)
focus = focus_selector.apply(pose)

nbr_12_selector = core.select.residue_selector.NeighborhoodResidueSelector()
nbr_12_selector.set_focus(focus)
nbr_12_selector.set_distance(12)
nbr_12_selector.set_include_focus_in_subset(True)

######## Task operations #######
initCommandLine = core.pack.task.operation.InitializeFromCommandline()
repackingRLT = core.pack.task.operation.RestrictToRepackingRLT()
repack_neigh_12 = core.pack.task.operation.OperateOnResidueSubset(repackingRLT,nbr_12_selector)
no_repackingRLT = core.pack.task.operation.PreventRepackingRLT()
no_repack_everythingElse = core.pack.task.operation.OperateOnResidueSubset(no_repackingRLT,nbr_12_selector, True) #flip_subset: True
#### packer_tasks
taskOper = core.pack.task.TaskFactory()
taskOper.push_back(initCommandLine)
taskOper.push_back(repack_neigh_12)
taskOper.push_back(no_repack_everythingElse)

 

Thank you again

Fri, 2023-08-11 10:57
karenjgonzalez