PCA

Principal Components

In this directory you find the two final principal component projections used in Nagel et al. 2023 and the script perform_pca to reproduce them.

Workflow to Create PCs

Here is a brief summary of how the two files were generated. For a more detailed description, please take a look at the publication above.

• hp35.dihs.res3-33.shifted.gaussian10f.proj.1-4
  1. Discarding angles of residue 2 and 34, $\phi_2, \psi_2, \phi_{34}, \psi_{34}$
  2. Apply Gaussian filtering with $\sigma=2\text{ns}$
  3. Perform PCA, here we do not need using dPCA+ because the dihedrals are already maximal gap shifted
  4. Extract first 4 PCs
• hp35.mindists2.gaussian10f.proj.1-5
  1. Apply Gaussian filtering with $\sigma=2\text{ns}$
  2. Perform conPCA
  3. Extract first 5 PCs

Reproduce the Results

To reproduce these results you simply have to run

# this will download and compile all needed files
bash perform_pca -c 1

This creates the directory create_pca_nagel23 with the two PCs projections, including all intermediate steps.