Electronic Structure Analysis (PyMOL)

This page covers electronic structure visualization using PyMOL, including molecular orbitals and spin density plots.

Molecular Orbital (MO) Jobs

Generate molecular orbital visualizations for frontier orbitals and other electronic states.

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

MO Options

Option	Type	Description
-n, --number	int	Specific MO number to visualize
-h, --homo	bool	Plot HOMO (default: disabled)
-l, --lumo	bool	Plot LUMO (default: disabled)

Note

MO jobs inherit all visualization options including styling, ray tracing, and surface rendering.

Basic Usage

Standard MO visualization:

chemsmart run mol -f calculation.log mo

HOMO visualization:

chemsmart run mol -f molecule.log mo -h

LUMO visualization:

chemsmart run mol -f molecule.log mo -l

Specific orbital:

chemsmart run mol -f molecule.log mo -n 5

Spin Density Jobs

Generate spin density visualizations for open-shell systems.

chemsmart run [OPTIONS] mol [MOL_OPTIONS] spin

Note

Requires both .log and .chk files in the same folder. If -l/--label is provided, CHEMSMART still processes files from the source filename basename (for example, output.log -> output.chk/output.fchk), while the final spin output/session filename follows the custom label.

Spin density jobs inherit all visualization options.

Basic Usage

Standard spin density:

chemsmart run mol -f radical.log spin

With ray tracing:

chemsmart run mol -f radical.log spin -t

With custom output label while still processing source files:

chemsmart run mol -f output.log -l new_name_new_spin_isovalue spin -i 0.1

This command processes output.log (and related output.chk/output.fchk) and writes the spin session as new_name_new_spin_isovalue.pse.