NCI Surface¶

Note

Surface plots are schematic 2D representations suitable for figures. For quantitative isosurface analysis, use a dedicated 3D viewer (VMD, PyMOL).

Visualise non-covalent interaction surfaces from a signed colouring field as the main input plus a second cube that defines the surface geometry.

--nci-surf now auto-classifies the surface cube as either:

low_field: points of interest are low, so the surface is extracted with data < iso
high_field: points of interest are high, so the surface is extracted with data > iso

This means the same flag works for both low-field analyses such as standard NCIPlot, and high-field analyses such as Multiwfn-style δg surfaces.

For standard NCIPlot output, use sign(λ₂)·ρ density as the main input and reduced density gradient as --nci-surf. These cubes are typically classified as low_field.

As an alternative analysis technique, Multiwfn-style δg surfaces use sl2r.cub as the main input and dg.cub, dg_inter.cub, or dg_intra.cub as --nci-surf. These cubes are typically classified as high_field.

Python. All xyzrender flags below map 1:1 to keyword arguments on render(). The Python kwarg matching --nci-surf is nci= (path to the gradient/δg cube): render(load("dens.cube"), nci="grad.cube", iso=0.3, nci_mode="pixel"). See the Python API guide.

Note

The default --iso values are starting points, not universal thresholds. They reflect the original NCIPLOT (RDG = 0.3) and Multiwfn IGMH (δg = 0.005) literature conventions. In practice you will need to tune --iso per cube — especially for IGMH, where dg_intra cubes have a much larger value range than dg_inter and typically need --iso between 0.05 and 0.3 for clean surfaces.

The surface is rendered as individual flat-filled patches per interaction region. Coloring is based on the sign of λ₂ weighted by density: blue = strong attractive (H-bond), green = weak/vdW, red = repulsive (steric).

H-bond (base pair)	π-stacking (phenol dimer)

# avg coloring (default): blue=H-bond, green=vdW, red=steric
xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube -o base-pair-nci_surf.svg
xyzrender phenol_di-dens.cube --nci-surf phenol_di-grad.cube -o phenol_di-nci_surf.svg

# per-pixel (more detail)
xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube --nci-mode pixel

# flat color (default: forestgreen)
xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube --nci-mode uniform

# flat color with custom colour
xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube --nci-mode teal

As an alternative analysis technique, IGMH-style interaction surfaces can be similarly visualised using --nci-surf alongside an sl2r.cub colouring field. The examples below use phenol dimer dg_inter and dg_intra cubes to show intermolecular and intramolecular interactions separately.

IGMH Inter (`dg_inter`, `--iso 0.005`)	IGMH Intra (`dg_intra`, `--iso 0.2`)

# intermolecular interaction surface
xyzrender phenol_di-sl2r.cub --nci-surf phenol_di-dg_inter.cub --iso 0.005 -o phenol_di_igmh_inter.svg

# intramolecular interaction surface
xyzrender phenol_di-sl2r.cub --nci-surf phenol_di-dg_intra.cub --iso 0.2 -o phenol_di_igmh_intra.svg

Coloring modes (--nci-mode):

Pixel (base pair)

xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube --nci-mode pixel -o base-pair-nci_pixel.svg

Mode	Description
`avg` (default)	Each NCI lobe filled with its mean `sign(λ₂)·ρ`: blue = H-bond, green = vdW, red = steric
`pixel`	Per-pixel `sign(λ₂)·ρ` raster — shows intra-lobe variation
`uniform`	Flat single color for all NCI regions (default: `forestgreen`)
colour	Any colour name or hex — shorthand for uniform mode with that colour

Surface styles also work on NCI patches:

Mesh

xyzrender base-pair-dens.cube --nci-surf base-pair-grad.cube --surface-style mesh

All interaction surface flags:

Flag	Description
`--nci-surf SURFACE_CUBE`	Interaction surface cube file. Auto-classified as `low_field` or `high_field` from the cube values
`--nci-mode MODE`	Coloring: `avg` (default), `pixel`, `uniform`, or a colour name/hex
`--iso`	Surface isovalue threshold (starting point — tune per cube). Low-field (NCIPLOT RDG) renders regions below the cutoff (default `0.3`). High-field (Multiwfn IGMH δg) renders regions above the cutoff: default `0.005` for `dg_inter`; `dg_intra` typically needs `0.05`–`0.3`
`--opacity`	Surface opacity multiplier (default: 1.0)
`--surface-style STYLE`	`solid` or `mesh` recommended; `contour`, `dot` also available. These use avg lobe colour
`--nci-cutoff CUTOFF`	Density magnitude cutoff (advanced — not needed for standard NCIPLOT output)

Sample structures from NCIPlot.