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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