Atom Colormap

Color atoms by a per-atom scalar value (e.g. partial charges, NMR shifts, Fukui indices) using a colormap palette.

Python. All xyzrender flags below map 1:1 to keyword arguments on render(). Two shapes differ from the CLI:

  • --cmap FILE → either cmap="charges.txt" (path) or cmap={1: 0.5, 2: -0.3} (1-indexed dict, no file needed)

  • --cmap-range VMIN VMAX → cmap_range=(-0.5, 0.5) (tuple)

render(mol, cmap={1: 0.5, 2: -0.3, 3: 0.04}, cmap_range=(-0.5, 0.5), cbar=True)
render(mol, cmap="charges.txt", cmap_symm=True, cmap_palette="coolwarm")

Mulliken charges (rotation)

Symmetric range

With colorbar

Mulliken charges (rotation)

Symmetric range

With colorbar

 
xyzrender caffeine.xyz --hy --cmap caffeine_charges.txt --gif-rot -go caffeine_cmap.gif
xyzrender caffeine.xyz --hy --cmap caffeine_charges.txt --cmap-range -0.5 0.5
xyzrender caffeine.xyz --hy --cmap caffeine_charges.txt --cbar

The colormap file has two columns — 1-indexed atom number and value. Any extension works. Header lines (first token not an integer), blank lines, and # comment lines are silently skipped.

# charges.txt
1  +0.512
2  -0.234
3   0.041

  • Atoms in the file: colored by the selected palette (default: Viridis — dark purple → blue → green → bright yellow)

  • Atoms not in the file: white (#ffffff). Override with "cmap_unlabeled" in a custom JSON preset

  • Range defaults to min/max of provided values; use --cmap-range vmin vmax for an explicit range or --cmap-symm for a symmetric range about zero

Flag

Description

--cmap FILE

Path to colormap data file (two-column: atom index, value)

--cmap-range VMIN VMAX

Override colormap range (useful for symmetric scales, e.g. -0.5 0.5)

--cmap-symm

Symmetric range about zero: `[-max(

--cmap-palette NAME

Colormap palette (default: viridis)

--cbar

Add a vertical colorbar on the right showing the data range

--label-size PT

Font size for colorbar tick labels (and all other labels)

Recommended palette set for xyzrender:

  • Best for --cmap: viridis, plasma, coolwarm

  • Best for ESP: rainbow, coolwarm, RdBu