Path B - Module 29: PDB Bioassemblies & AltLocs#

Many high-resolution industrial enzymes are solved using X-ray crystallography. These files often contain Alternate Locations (AltLocs), which are ghost-like representations of atoms that exist in more than one position in the crystal. PDB paths and PDB text share the native PDBFileHandler, so every native target receives the same normalized records and diagnostics.

In this module, you will learn to clean these ambiguities to have a physically consistent starting point for your PETase simulation.

import molsysmt as msm
from molsysmt import systems

# Load a structure with alternate locations from the Protein Data Bank
pdb_id = 'pdb_id:1BRS'
pdb_text = msm.convert(pdb_id, to_form='string:pdb_text')
molsys = msm.convert(pdb_text, to_form='molsysmt.MolSys')

1. Identifying the Disorder#

Let’s see if our system has atoms with multiple locations. These are problematic for most force fields.

alternate_locations = msm.get(molsys, alternate_location=True)
n_alternate_atoms = sum(len(entries) for entries in alternate_locations or [])

print(f"Found {n_alternate_atoms} atoms with multiple positions in the crystal.")

2. Solving AltLocs#

The function solve_atoms_with_alternate_location() activates the position with the highest occupancy for each canonical atom site and prefers label A when occupancies tie. All variants remain available in Structures.alternate_location.

print(msm.get(molsys, alternate_location=True))

msm.build.solve_atoms_with_alternate_location(molsys)

print("Alternate locations resolved without changing the topology atom count.")

3. Biological Assembly check#

Is the PETase active as a monomer or a dimer? MolSysMT reads PDB REMARK 350 symmetry operators into Structures.bioassembly, remaps them when atoms are extracted, and can generate the functional unit from those native instructions.

# Make the biological assembly
full_unit = msm.build.make_bioassembly(molsys)

msm.info(full_unit, element='chain')

🏁 END OF PHASE 3: THE VIRTUAL LAB#

Congratulations! You have completed the structural preparation of your industrial biocatalyst. You have:

  1. Isolated the PETase.

  2. Audited and Repaired the missing atoms.

  3. Engineered a new disulfide bridge for thermal stability.

  4. Synthesized a purification tag and a BHET substrate.

  5. Solvated and Patched the system for a professional report.

Now that your industrial model is ready, we enter Phase 4: Data Analyst, where we will measure if our engineering actually improved the enzyme’s geometry.