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Minimizing a Symmetric Structure

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Minimizing a Symmetric Structure
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Hi, I have a structure with two chains (1 and 2 ) which are identical. My goal is to minimize its structure using FastRelax with a symmetry constraint.

Creating symmetry file:

make_symmdef_file.pl -p Data/2mcg.pdb -a 1 -i 2 > Data/2mcg.symm

Structure minimization:

import pyrosetta
from pyrosetta import rosetta

id = '2mcg'

pose = pyrosetta.pose_from_pdb(f'Data/{id}_symm.pdb')
symm_data = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
symm_data.read_symmetry_data_from_file(f'Data/{id}.symm')
pyrosetta.rosetta.core.pose.symmetry.make_symmetric_pose(pose, symm_data)

rel = rosetta.protocols.relax.FastRelax()
rel.apply(pose)  # Segmentation Fault

But I get segmentation fault at the line specified above.

Moreover, I get the following error when I score the symmetric pose:

import pyrosetta
from pyrosetta import rosetta

id = '2mcg'

pose = pyrosetta.pose_from_pdb(f'Data/{id}_symm.pdb')
symm_data = pyrosetta.rosetta.core.conformation.symmetry.SymmData()
symm_data.read_symmetry_data_from_file(f'Data/{id}.symm')
pyrosetta.rosetta.core.pose.symmetry.make_symmetric_pose(pose, symm_data)

scorefxn = pyrosetta.get_fa_scorefxn()
scorefxn(pose)  # Error Line
RuntimeError: 

File: CountPairFactory.cc:220
[ ERROR ] UtilityExitException
ERROR: Assertion `res2.is_bonded(res1)` failed.

 

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Wed, 2023-08-02 11:10
ammar.x.gilani