Path D - Module 35: Principal Components (PCA) & Axes

Identify the Gating Modes of the channel. In this module, you will learn to use PCA to visualize the opening and closing of the pore.

import molsysmt as msm
from molsysmt import systems
system = [systems['POPC membrane']['popc_membrane.h5msm'], systems['POPC membrane']['popc_membrane.dcd']]
eigenvectors, eigenvalues = msm.structure.principal_component_analysis(system, selection='atom_name=="CA"')
# PC1 is eigenvectors[0]; eigenvalues[0] is its variance in nm**2.