Path C - Module 29: PDB Bioassemblies & AltLocs

High-resolution Mpro structures often have disordered regions in the binding pocket. In this module, you will learn to choose the correct crystallographic locations to avoid clashing with your inhibitor. PDB paths and PDB text share the native PDBFileHandler. Import keeps each alternate site canonical, retains formal charges and explicit CONECT/LINK/SSBOND chemistry, and materializes REMARK 350 biological-assembly operators.

import molsysmt as msm

# Load Mpro (6LU7) and solve AltLocs
molsys = msm.convert('pdb:6LU7', to_form='molsysmt.MolSys')
alternate_locations = msm.get(molsys, alternate_location=True)
if alternate_locations is not None and any(alternate_locations):
    msm.build.solve_atoms_with_alternate_location(molsys)

print("Binding site cleaned from AltLoc ambiguities.")