ChimeraX pyLovo

Protein sub structure alignment

Installation

First install ChimeraX here

Then download the alphaspace and store it in your preferred location.

Open ChimeraX and in the command line, type:

devel install pylovo_installation_folder

To reinstall after any change in code, simply repeat the command.

Usage

For protein with different topology

lovo match_atoms to ref_atoms n_cluster 3 plot true

For example:

lovo #2 to #1 would align all atoms of model 2 to model 1 lovo #2@Ca to #1@Ca would align just Ca carbon atoms of model 2 to model 1

For trajectory

When two or more structures are from a trajectory, meaning they have exactly same topology, you can align them with this command:

lovo traj match_atoms to ref_atom n_cluster 3 plot true

Use to option to specify which snapshot to align to, if not provided it defaults to first snapshots

Use n_clusters to specify how many clusters to produce, default is 3, with core, intermediate and flexible regions

You can also produce plots with plot true command

This program is based on the MDlovo paper:

L. Martínez, Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One 10(3): e0119264, 2015.