Reaction Analysis (PyMOL)

This page covers reaction pathway visualization using PyMOL, including IRC trajectories and molecular dynamics during chemical reactions.

IRC Jobs

Generate IRC movies and trajectory visualizations.

chemsmart run [OPTIONS] mol [MOL_OPTIONS] irc [SUBCMD_OPTIONS]

IRC Options

Option	Type	Description
-r, --reactant	string	IRC file for reactant side
-p, --product	string	IRC file for product side
-a, --all	string	File containing complete IRC trajectory

Note

IRC jobs inherit all visualization options.

Basic Usage

Standard IRC visualization:

chemsmart run mol -f irc_output.log irc

With separate reactant/product files:

chemsmart run mol -f ts_structure.xyz irc -r reactant.log

From complete trajectory:

chemsmart run mol -f ts.xyz irc -a full_irc_trajectory.log