3D Renders from QM Output Files: The xyzrender Tool
You ran the calculation. Now make it look like a paper figure. ChemIllusion's 3D / QM Render tool uses xyzrender to turn XYZ coordinates, SDF, MOL, and PDB files into publication-quality molecular graphics in seconds — no separate visualization pipeline required.
Running a quantum chemistry calculation is one thing. Turning the output into a figure you can put in a paper, a slide, or a graphical abstract is another. Most visualization tools assume you already know PyMOL, VMD, or UCSF Chimera. If you just want a clean 3D render of a small molecule from a coordinate file, the overhead is real.
The 3D / QM Render tool in ChemIllusion closes that gap. Upload a coordinate file, pick a preset, and place the result on your canvas. No separate software. No command line.
Learn-series walkthrough: ethanol XYZ coordinates rendered as a publication-quality 3D figure using the paton preset.
The gap between coordinates and figures
A QM output file from Gaussian, ORCA, or NWChem contains everything needed to describe a molecule's geometry: element symbols and Cartesian coordinates for every atom, often alongside optimized bond lengths and angles. What it does not contain is a figure. The raw text is precise and correct, but it communicates nothing to an audience looking at a slide or a paper.
The standard workflow — export to XYZ, open in a visualization program, adjust rendering settings, export image — works, but it is a detour. For a researcher preparing a graphical abstract or an instructor building a lecture slide, the goal is the figure, not the software literacy test.
How xyzrender works
The tool is built on xyzrender (v0.3.1) by Dr. Alister Goodfellow, described as “Publication-quality molecular graphics” for small-molecule coordinate files. Under the hood, xyzrender uses xyzgraph to construct a molecular connectivity graph directly from raw Cartesian coordinates — inferring bonds from interatomic distances without requiring an explicit connectivity table. It uses cclib to parse quantum chemistry output files from codes like Gaussian, ORCA, and NWChem, extracting the optimized geometry from whatever format the calculation produced. The molecular graph is then rendered via graphrc with resvg-py handling SVG-to-PNG conversion for high-resolution raster output.
The result is a render that is derived from the actual computed geometry — not a 2D depiction, not a stock structure, but the specific conformation the calculation optimized to. That distinction matters for papers and graphical abstracts where the geometry itself is part of the scientific content.
Using the tool in ChemIllusion
Open the Generator and ask the assistant to open the 3D / QM Render tool, or select it from the toolbar. Upload a coordinate file — XYZ, SDF, MOL, or PDB are all supported. The tool parses the file, infers connectivity, and renders a preview using the selected preset. From there:
Rotate the model to the orientation that communicates the relevant geometry.
Switch presets to compare rendering styles — paton for publication figures, vdw for space-filling volume, skeletal for clean line representations, tube for backbone geometry.
Click Add to canvas to place the render as an editable object with auto-generated alt text.
For researchers preparing graphical abstracts, the render can be placed alongside reaction arrows, energy diagrams, and other canvas objects. For instructors, it slots into the same workflow as CineMol 3D space-filling models and Newman projections — all produced on the same canvas, all exportable with built-in accessibility metadata.
Render presets
The tool ships with four presets tuned for different use cases:
paton — gradient-shaded spheres with a warm highlight and subtle glow. The default for publication figures and graphical abstracts.
vdw — van der Waals space-filling, where each atom is rendered at its full van der Waals radius with no gaps. Emphasizes molecular volume and steric crowding.
skeletal — a 3D skeletal representation with atom labels, closer to a perspective line drawing than a space-filling render. Useful when bond connectivity needs to be visible.
tube — smooth tube/cylinder backbone with no explicit atom spheres. Clean for showing overall molecular shape without element-by-element detail.
Try it
If you have a coordinate file — from a geometry optimization, a structure database, or a PDB download — bring it into the Generator and render it in under a minute.
Supports XYZ, SDF, MOL, and PDB. No account required for your first render.