PACKMAN Compliance Analysis Tutorial

IMPORTANT NOTE: This tutorial is for the publication version (v1.1.1). For the latest tutorial, please check the tutorial sections on the following link:

Step 1.1 Import the 'molecule' submodule from PACKMAN. (If PACKMAN is not installed, please follow the link:

Step 1.2 Download the structure from PDB and save it with the appropriate extension.

Step 1.3 Load the structure using the submodule

Step 2.1 Import 'anm' submodule from PACKMAN.

Step 2.2 Load the C-Alpha atoms of the molecule from the first model. For further information about the atoms selection and 'molecule' object functions, please read the PACKMAN 'molecule' tutorials.

Step 2.3 Get the C-Alpha atom coordinates.

Step 2.4 Build the ANM model of the selected atoms. With appropriate power (Please refer to the Publication)

Step 3 Calculate the Hessian Matrix, Decompose it and Run the stiffness and compliance analysis.

Step 4 Extract and store the maps and profiles for the visualization.

Step 5 Import any visualization package such as seaborn and visualize the stiffness profile.

Step 6 Similarly, for the compliance profile

Step 7 Visualize the profiles and compare them with the experimental B-factors.

Step 8 Calculate the Pearson Correlation Coefficient between any profile and the experimental B-factors.