Unable to find residue ... after preparation error

[dargen3]

Hello,

quite often moleculekit returns a strange error like "RuntimeError: Unable to find residue MET 1 A 0 after preparation". I would like to ask for an explanation of what this error means, and if there is anything I can do to make moleculekit able to process the structure.

Code for reproduction (the structure was downloaded from PDB):

from moleculekit import molecule as moleculekit_PDB
from moleculekit.tools.preparation import systemPrepare as moleculekit_system_prepare

molecule = moleculekit_PDB.Molecule("2ehu.pdb")
prepared_molecule, details = moleculekit_system_prepare(molecule,
                                                        pH=7,
                                                        hold_nonpeptidic_bonds=False,
                                                        ignore_ns_errors=True,
                                                        _molkit_ff=False,
                                                        return_details=True)
prepared_molecule.write(f"{self.data_dir}/output.pdb")

[stefdoerr]

The residue numbering in that PDB is a pure mess

I don't know why it's so bad but propka tends to have issues with broken structures. You can try cleaning it up, fixing it a bit and it might work.
Defining chains differently worked for me

from moleculekit.tools.autosegment import autoSegment2

molecule = moleculekit_PDB.Molecule("2ehu")
molecule.filter("protein")
molecule = autoSegment2(molecule)

But the autosegmentation is also wrong because it creates two chains with a single residue. So I think this structure requires some manual cleaning / chain definition to work.

[dargen3]

Thank you for your quick reply! PDB is full of all kinds of bugs.