Analysis and Export

Taking Measurements

Click atoms in the viewport to select them, then read off the geometry:

Atoms selected	What you see
2	Distance (Å)
3	Bond angle (°)
4	Dihedral angle (°)

Hold Shift and click to add atoms to the current selection.

Display Options

Use the display controls to change how the structure is rendered:

• Van der Waals spheres — space-filling view, useful for inspecting steric contacts
• Show hydrogens — toggle hydrogen visibility on and off
• Convex hulls — highlight detected aromatic or ring-like regions when available
• Conformer overlay — compare multiple geometries at once
• Stereochemistry labels — show stereochemical assignments when annotated data is available
• Non-covalent interactions — show contact annotations when the data is available
• Mulliken charges — color atoms by Mulliken partial charge and show a matching legend when supported QM output is loaded
• COSMO surface — render a solvation surface when compatible data is loaded
• Volumetric surfaces — toggle cube-derived HOMO, LUMO, density, and ESP datasets individually when present
• Force arrows — display force vectors on atoms after a single point energy calculation
• TS analysis bonds — highlight bonds being formed or broken in a transition state
• Auto-rotate — continuous rotation for presentations, with vertical and diagonal options

Cube Surface Visualization

When Gaussian cube data is loaded, the viewer adds a dedicated surface control block and renders each supported dataset as its own overlay layer.

Supported cube-derived views:

• HOMO / LUMO — positive and negative orbital lobes
• Density — electron density isosurface
• ESP — electrostatic potential mapped onto a surface, ideally using a matching density cube

Viewer behavior:

• Each available cube dataset gets its own display toggle.
• ESP surfaces show a matching color legend in the viewer.
• The same upload can expose multiple datasets at once when related cube files are provided together.

Molecular Information

The viewer displays key properties of the loaded structure:

• Chemical formula — composition of the current geometry
• SMILES — canonical SMILES string with a copy button
• Charge and multiplicity — shown when set
• Point group and symmetry number — shown when symmetry metadata is available

Structure History

Recent structures are stored in the browser so the viewer can restore where you left off. This is useful when switching between loaded files, edited geometries, and newly computed results within the same session.

Exporting

Geometry Export

Export the current geometry when you want to save it or use it in another tool.

Format	Extension
XYZ	.xyz
CIF	.cif
SDF / MOL	.sdf, .mol
PDB	.pdb
VASP	.vasp
Cube	.cube

Available export formats depend on what is currently loaded.

Image Export

Save the current 3D view as a PNG or GIF image using the save image button.

Share Link

Generate a shareable URL that encodes the current structure so others can open it directly in the viewer.

The Share button opens a small menu with three one-click options:

• Copy link — copies the direct share URL
• Embed as badge — copies a branded badge snippet that links back to the shared view
• Embed as viewer — copies an iframe snippet for embedding the interactive branded molecule viewer on a web page

Example Badge

Markdown

Use this in README.md files, issues, pull requests, and other Markdown surfaces:

[![View on Atomiverse](https://atomiverse.com/assets/atomiverse-share-badge.svg)](https://atomiverse.com/viewer?share=YOUR_SHARE_ID)

HTML

Use this on any web page:

<a href="https://atomiverse.com/viewer?share=YOUR_SHARE_ID" target="_blank" rel="noopener noreferrer">
  <img src="https://atomiverse.com/assets/atomiverse-share-badge.svg" alt="View on Atomiverse" height="20">
</a>

Replace YOUR_SHARE_ID with the share ID created by the viewer. The built-in Embed as badge action copies a ready-to-paste version automatically.

Embedded Viewer

Use this on any web page when you want to showcase an interactive shared structure inline:

<iframe
  src="https://atomiverse.com/viewer?share=YOUR_SHARE_ID&embed=1"
  title="Atomiverse molecule viewer"
  loading="lazy"
  referrerpolicy="strict-origin-when-cross-origin"
  allow="fullscreen"
  allowfullscreen
  style="width:100%;height:420px;border:0;border-radius:18px;overflow:hidden"
></iframe>

The built-in Embed as viewer action copies a ready-to-paste version of this snippet automatically.