[PyMOL] H-bond data extraction

[Neena S. E. <nee...@gm...>]

Hello PyMOL users,

This is not a question related to PyMOL, but I was wondering if someone can
help me or guide me to the appropriate resource.

I extracted two types of H-bond occupancy data (donor: Lysine side chain
and backbone amide NH, with backbone carbonyl CO as acceptor) from two
different trajectories of the same peptide, centroid structures from
predominant cluster of each trajectory shown in each row. These structures
just differ by dihedral angles across a few residues.

Question: What is the best way to quantify relative strength of total
intramolecular hydrogen bonding between these two trajectories?
[image: image.png]
Many thanks,
Neena
Graduate student, U of T