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set_torsion_angle error

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set_torsion_angle error

Hi all,

I created a customized ligand, and we want to sample different rotamers around certein bonds by changing the torsion angles. And below is what we have done and we ran into an issue:

atom1 = AtomID(13,1)

atom2 = AtomID(14,1)

atom3 = AtomID(15,1)

atom4 = AtomID(16,1)

old_torsion_angle = pyrosetta.rosetta.core.conformation.Conformation().torsion_angle(atom1, atom2, atom3, atom4)

print (old_torsion_angle)

new_torsion_angle = pyrosetta.rosetta.core.conformation.Conformation().set_torsion_angle(atom1, aomt2, atom3, atom4, pi/4)

print (new_torsion_angle)


Then it outputs Segmentation fault (core dump)

Is there anyone that can give us some suggestion? Thank you all




Post Situation: 
Tue, 2019-07-09 12:43

The biggest issue you have is that `pyrosetta.rosetta.core.conformation.Conformation()` creates a brand new (empty) conformations. It doesn't have a residue 1, atom 16 -- it doesn't have any atoms at all!

What you'll need to do is to load a molecular system into a conformation. The way to do this is to load a structure (e.g. from a PDB) into a Pose, and then work on the pose. Often you'll need to be careful that you're working on the system you think you are, and that it has all the atoms and residues in the places where you think they should be. You can run into odd behavior if that assumption is violated.

Tue, 2019-07-09 13:25

Thank you for your reply, your reply really helped, that was one point that we missed. Thank you Thank you so much

Wed, 2019-07-10 09:18