Path A - Module 22: Structural Auditing (Diagnostics)#

A Master never trusts a file blindly. Before you start building your therapeutic peptide or running a simulation, you must know what is missing or broken in your target.

In this module, you will perform a complete audit of the Amyloid-Beta fibril (2BEG).

import molsysmt as msm
from molsysmt import systems

# Let's load the full fibril again
fibril = msm.convert('pdb:2BEG', to_form='molsysmt.MolSys')

1. The Hydrogen Check#

Most NMR structures like 2BEG might have hydrogens, but X-ray structures usually don’t. Hydrogens are essential for calculating hydrogen bonds or running simulations.

has_h = msm.build.has_hydrogens(fibril)
print(f"Does the 2BEG fibril have hydrogens? {has_h}")

2. Missing Residues#

Often, experimentalists cannot resolve certain parts of a protein (like flexible loops). MolSysMT can tell you which residues are theoretically in the sequence but missing in the coordinates.

missing_res = msm.build.get_missing_residues(fibril)
print(f"Missing residues summary: {missing_res}")

3. Missing Heavy Atoms#

Sometimes a residue is present, but it’s missing some sidechain atoms. This is a “broken” residue that needs repair.

missing_atoms = msm.build.get_missing_heavy_atoms(fibril)
print(f"Are there any missing heavy atoms? {len(missing_atoms) > 0}")
if missing_atoms:
    print(f"Details: {missing_atoms}")

4. Non-Standard Residues#

Audit if there are cofactors, ions, or water molecules that might interfere with your analysis.

non_std = msm.build.get_non_standard_residues(fibril)
print(f"Non-standard residues found: {non_std}")

🏆 Path A Challenge: The Structural Spy#

  1. Load the PDB ID 'pdb:181L' (our old Lysozyme training system).

  2. Check if it has hydrogens.

  3. Use get_non_standard_residues() to identify all the ligands and ions in it.

  4. Audit if it has any missing residues in its sequence.

Great! You are now an expert in structural diagnostics. In Module 23, we will finally get our hands dirty and Repair the fibril by adding what’s missing and mutating residues.