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 Electronic Structure Analysis (PyMOL)
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This page covers electronic structure visualization using PyMOL, including molecular orbitals and spin density plots.

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 Molecular Orbital (MO) Jobs
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Generate molecular orbital visualizations for frontier orbitals and other electronic states.

.. code:: bash

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

MO Options
==========

.. list-table::
   :header-rows: 1
   :widths: 30 15 55

   -  -  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:

.. code:: bash

   chemsmart run mol -f calculation.log mo

HOMO visualization:

.. code:: bash

   chemsmart run mol -f molecule.log mo -h

LUMO visualization:

.. code:: bash

   chemsmart run mol -f molecule.log mo -l

Specific orbital:

.. code:: bash

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

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 Spin Density Jobs
*******************

Generate spin density visualizations for open-shell systems.

.. code:: bash

   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:

.. code:: bash

   chemsmart run mol -f radical.log spin

With ray tracing:

.. code:: bash

   chemsmart run mol -f radical.log spin -t

With custom output label while still processing source files:

.. code:: bash

   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``.