Open rdkibler opened 3 years ago
Is there a residue named vrt in your pdb? Basically you can’t have your residue selectors select residues without backbone atoms.
There are not ATOM lines in the pdb file with residues named vrt, but the pose in pyrosetta does have virtual residues after symmetrization
Ok. Somehow you will have to make the residue selectors such that they avoid those residues. Something like a residue index selector is a work around.
adding if not residue.is_virtual_residue()
to the first two list comprehensions in the apply()
func in stapler.py fixes this
def apply(self, pose):
xyzs_a = np.array([[residue.atom(atom).xyz() for atom in self.atom_selectors[0]] for residue in pose.residues if not residue.is_virtual_residue()])
xyzs_b = np.array([[residue.atom(atom).xyz() for atom in self.atom_selectors[0]] for residue in pose.residues if not residue.is_virtual_residue()])
I am attempting to staple a symmetric interface using a bit of code thuddy sent me, but I'm getting an error related to virtual residues not having atoms. Here's the code:
And here is the error.log. The important bit is: