Path D - Module 21: Surgical Extraction & Deletion#

Welcome, Mechanic. Your mission is to study the ionic flux through a Potassium Channel embedded in a cellular membrane. These systems are massive and complex, involving proteins, lipids, ions, and water.

In this module, you will learn to use extract() and remove() to simplify these large membrane models and focus on the pore.

import molsysmt as msm
from molsysmt import systems

# Load a pre-equilibrated membrane system from the database
molsys = systems['POPC membrane']['popc_membrane.dcd']
topo = systems['POPC membrane']['popc_membrane.h5msm']
system = [topo, molsys]

1. Identifying the Components#

Membrane systems are heterogeneous. Let’s see the entity inventory.

msm.info(system, element='entity')

2. Extracting a Membrane Patch#

Sometimes the system is too large for your workstation. You can extract() only the channel and a small neighborhood of lipids.

# Extract atoms within 2.0 nm of the Z-axis (the pore area)
pore_patch = msm.extract(system, selection='within 2.0 nm of molecule_type=="protein"')

print(f"Extracted atoms: {msm.get(pore_patch, element='system', n_atoms=True)}")
msm.view(pore_patch)

🏆 Path D Challenge: The Membrane Trimmer#

  1. Load the POPC membrane system.

  2. Use msm.remove() to delete all Water molecules (SOL) from the system to create a dry model.

  3. Use msm.extract() to isolate only the POPC lipids into a new object called bilayer.

  4. Verify with msm.info() that your bilayer contains 0 protein atoms.

You have isolated the nano-machine! In Module 22, we will perform a Structural Audit to ensure the channel tetramer is physically complete.