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 Interaction Analysis (PyMOL)
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This page covers non-covalent interaction visualization using PyMOL.

**********
 NCI Jobs
**********

Generate non-covalent interaction (NCI) plots for analyzing intermolecular and intramolecular interactions.

.. code:: bash

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

NCI Options
===========

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

   -  -  Option
      -  Type
      -  Description

   -  -  ``-i, --isosurface``
      -  float
      -  Isosurface value (default: 0.5)

   -  -  ``-r, --color-range``
      -  float
      -  Color ramp range (default: 1.0)

   -  -  ``-b, --binary``
      -  bool
      -  Two-color plot (default: disabled)

   -  -  ``--intermediate``
      -  bool
      -  Intermediate range colors (default: disabled)

.. note::

   NCI jobs inherit all visualization options.

Basic Usage
===========

Standard NCI plot:

.. code:: bash

   chemsmart run mol -f complex.xyz nci

Custom color range:

.. code:: bash

   chemsmart run mol -f complex.xyz nci -r 1.5

Binary color plot:

.. code:: bash

   chemsmart run mol -f hydrogen_bond.xyz nci -b

High-quality with ray tracing:

.. code:: bash

   chemsmart run mol -f complex.xyz nci -i 0.4 -t -s pymol