Path A - Module 21: Surgical Extraction & Deletion#

Welcome, Architect. Your mission is to destabilize the Amyloid-Beta (Aβ) fibril. These aggregates are the hallmarks of Alzheimer’s disease.

To design a drug or a peptide against them, you first need to isolate the target. In this module, you will learn to use the “scissors” of MolSysMT: extract() and remove().

import molsysmt as msm
from molsysmt import systems

1. Loading the Fibril#

We will use the PDB ID 2BEG, which represents a solid-state NMR structure of the Aβ(1-42) fibril. It is composed of 5 identical chains.

fibril = msm.convert('pdb:2BEG', to_form='molsysmt.MolSys')
msm.info(fibril)

2. Surgical Extraction#

The fibril is too large for our initial analysis. We want to work only with the central core (Chain 2). The function extract() creates a new, independent molecular system containing only your selection.

# Extract only the central chain
core_chain = msm.extract(fibril, selection='chain_index==2')

print(f"Original atoms: {msm.get(fibril, element='system', n_atoms=True)}")
print(f"Extracted atoms: {msm.get(core_chain, element='system', n_atoms=True)}")
msm.info(core_chain)

3. Deleting with remove()#

Sometimes it is easier to say what you don’t want. Let’s say we want to study the dimer formed by the first two chains. We can remove the rest.

# Remove everything except the first two chains
dimer = msm.remove(fibril, selection='chain_index > 1')

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

4. Why use Extract/Remove instead of Select?#

When you use select(), you just get a list of numbers. When you use extract() or remove(), MolSysMT rebuilds the topology:

  • Atom indices start from 0 again.

  • Residue and chain indices are cleaned up.

  • The result is a perfect, ready-to-use “Form”.

msm.view(dimer)

🏆 Path A Challenge: The Fibril Trimmer#

  1. Extract the last two chains of the 2BEG fibril into a new object called tail.

  2. Verify that tail has exactly 2 chains using msm.info().

  3. Use msm.view() to visualize your new truncated model.

You have successfully isolated your target. In Module 22, we will perform a Structural Audit to see if our target has any missing pieces before we start the repair.