Membrane-bound relaxation constrained by an ED map

[Anonymous]

I am energy minimising a membrane protein with the RosettaMP framework, but also constraining it to the electron density map.

I am creating the membrane chain vector thinggy by starting with an OPM database style PDB (protein placed ±14 Å xy plane but without the cute membrane marker atoms aren’t used) with the usual `pyrosetta.rosetta.protocols.membrane.AddMembraneMover(‘from_structure’)`, but then I am calling `pyrosetta.rosetta.protocols.simple_moves.AlignChainMover()` to move the pose (based on the peptide chain) to a pose in the ccp4 map.

`AddMembraneMover(‘from_structure’)` on a pose in the OPM database positioning generates an `out.span` which will result in a segfault when applied to the cpp4 map pose —both by writing `AddMembraneMover(‘out.span’)` or manually making a `SpanningTopology()` with various `.add_span(Span(..))`.

It “seems” to work, but it’s always hard to tell as there are lots of secret things going on. Say `AqueousPoreFinder`makes a position dependent `_DLPC_ellipse.dat` file, although I do not if this does anything.

However, what worries me is that the membrane namespace/module contains the movers `TranslationRotationMover`, `TranslationMover` and `RotationMover` —but require rototranslation matrices, so if I were to have gone down the rabbithole of 3D rototranslations, I’d have moved the map in gemmi.

So my question is: Is it okay to move a AddMembraneMover membrane chain vector thinggy with AlignChainMover?

The code simplified is the following:

import pymol2



# pdbblocks

with pymol2.PyMOL() as pymol:

pymol.cmd.load('homologue_phyre.pdb', 'phyre')

# remove rubbish parts

pymol.cmd.remove('resi 1-68 or resi 245-282 or resi 494-504')

# align

pymol.cmd.alter('*', 'chain="A"')

pymol.cmd.sort()

pymol.cmd.fetch('6C08')

pymol.cmd.align('phyre', '6C08 and chain C')

pymol.cmd.delete('6C08')

map_pdbblock = pymol.cmd.get_pdbstr()

pymol.cmd.load('OPM_6c08.pdb', 'OPM')

pymol.cmd.align('phyre', 'OPM')

pymol.cmd.delete('OPM')

mem_pdbblock = pymol.cmd.get_pdbstr()



# poses

map_pose = pyrosetta.Pose()

pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(map_pose, map_pdbblock)



mem_pose = pyrosetta.Pose()

pyrosetta.rosetta.core.import_pose.pose_from_pdbstring(mem_pose, mem_pdbblock)

addmem = pyrosetta.rosetta.protocols.membrane.AddMembraneMover('from_structure')

addmem.apply(mem_pose)



# align

ali = pyrosetta.rosetta.protocols.simple_moves.AlignChainMover()

ali.pose(map_pose)

ali.source_chain(1) # 0 for whole is a no as num res differs due to MEM resn

ali.target_chain(1)

ali.apply(mem_pose)



# the vector thing moved for sure:

import nglview

from IPython.display import display



view = nglview.show_rosetta(map_pose)

view.add_structure(nglview.RosettaStructure(mem_pose))

display(view)



# pore

pose = mem_pose

pyrosetta.rosetta.protocols.membrane.AqueousPoreFinder().apply(pose)



# scorefxn

scorefxnED = pyrosetta.create_score_function('mpframework_smooth_fa_2012')

ED = pyrosetta.rosetta.core.scoring.electron_density.getDensityMap('6c08.ccp4')

sdsm = pyrosetta.rosetta.protocols.electron_density.SetupForDensityScoringMover()

sdsm.apply(pose)

elec_dens_fast = pyrosetta.rosetta.core.scoring.ScoreType.elec_dens_fast

scorefxnED.set_weight(elec_dens_fast, 10)



# movemap

movemap = pyrosetta.MoveMap()

assert len(pyrosetta.rosetta.core.pose.get_chains(pose)) == 2, 'Not two chains'

v = pyrosetta.rosetta.core.select.residue_selector.ChainSelector(1).apply(pose)

mem_chain = pyrosetta.rosetta.core.pose.get_chain_from_chain_id(2, pose)

movemap.set_bb(allow_bb=v)

movemap.set_chi(allow_chi=v)

movemap.set_jump(False)



# relax

relax = pyrosetta.rosetta.protocols.relax.FastRelax(scorefxnED, 15)

relax.set_movemap(movemap)

relax.apply(pose)

 

 

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