Publication-quality molecular graphics rendering using xyzrender. Use when the user needs to create high-quality figures (SVG, PNG, PDF, GIF) for molecular structures, orbitals, surfaces, or animations from XYZ, PDB, Gaussian, ORCA, and other chemical file formats.
This skill provides a structured approach for using the xyzrender tool to create publication-quality molecular graphics. It handles everything from basic ball-and-stick models to complex electronic surfaces and animations.
For simple visualization of a molecular structure.
xyzrender molecule.xyz -o output.png
Use the paton preset for high-quality, glossy molecular models.
xyzrender molecule.xyz --config paton --hy -o figure.svg
Tip: Use SVG for vector graphics that can be further edited in tools like Inkscape or Illustrator.
Render dashed bonds for transition states or non-covalent interactions (NCI).
# Automated TS bond detection
xyzrender ts_geometry.xyz --ts -o ts_figure.png
# Automated NCI detection
xyzrender complex.xyz --nci -o nci_figure.png
Render electronic structure data from Gaussian/ORCA output or .cube files.
xyzrender mol.xyz orbital.cube --iso 0.05 --surf-style solid -o orbital.png
Generate rotating GIFs or vibrational modes.
# Rotation GIF
xyzrender molecule.xyz --gif-rot -go rotation.gif --frames 60
# Vibrational Mode (from QM output)
xyzrender orca.out --mode 1 --gif -go vibration.gif
--config paton for most publications, or --config flat for technical diagrams.--hy)? Are there lone pairs or NCIs to show?.svg for highest quality vector output or .png --dpi 300 for high-res raster.