Interaction Analysis (PyMOL)

This page covers non-covalent interaction visualization using PyMOL.

NCI Jobs

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

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

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.

Standard NCI plot:

chemsmart run mol -f complex.xyz nci

Custom color range:

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

Binary color plot:

chemsmart run mol -f hydrogen_bond.xyz nci -b

High-quality with ray tracing:

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