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Loading Structures

There are three main ways to get a structure into the viewer.

Paste​

Copy coordinates from another tool and paste them into the input panel. Atomiverse detects the format automatically. Multi-frame XYZ files are loaded as trajectories.

Supported formats: XYZ, CIF, SDF, MOL, PDB

Upload​

Click the upload button and select a file from disk. Best for larger structures or files saved from other tools.

Supported formats: XYZ, CIF, SDF, MOL, PDB, Cube

Cube uploads​

The viewer can build volumetric surface overlays from Gaussian cube files. You can upload one cube or a related bundle of cubes in a single action.

Supported cube workflows:

  • HOMO and LUMO orbital cubes
  • Electron density cubes
  • ESP cubes, ideally paired with a matching density cube

Behavior notes:

  • Multi-file upload is supported for related cube datasets such as density + ESP.
  • Surface-specific display options appear automatically when cube data is present.
  • Matching legends are shown for color-mapped surfaces such as ESP.

Identifier​

The Identifier tab combines direct structure input with external molecule search so the import flow stays in one place.

Direct input​

Type or paste a SMILES string to generate a 3D structure directly. Atomiverse adds hydrogens and generates 3D coordinates before loading the result into the viewer. Multi-molecule systems use dot-separated SMILES (for example O.O for two water molecules).

note

SMILES conversion uses a server-side step. The geometry it returns is a reasonable starting point — you may want to relax it in Build Mode before running calculations.

Search PubChem / ChEMBL​

Use the search block in the same tab when you want to look up a molecule from external databases before loading it.

Supported queries include:

  • Common names such as aspirin or caffeine
  • SMILES
  • InChI and InChIKey
  • PubChem CID values such as CID2244
  • ChEMBL identifiers such as CHEMBL25

The source selector lets you choose:

  • Auto to search across supported sources
  • PubChem to search only PubChem
  • ChEMBL to search only ChEMBL

Search results are shown as candidate cards with the most useful identifying details. If several plausible matches are returned, Atomiverse shows them and lets you choose which one to load instead of silently picking a structure for you.

When a result is loaded, it behaves like other imported molecules in the viewer and keeps its source metadata attached.

Resolution behavior​

  • Clear empty states are shown when nothing matches the query
  • Temporary source failures are surfaced as useful error messages
  • Ambiguous results stay user-selectable rather than being auto-resolved

Navigating the 3D View

ActionHow to do it
RotateLeft-drag (or one-finger drag on touch)
PanRight-drag (or two-finger drag on touch)
ZoomScroll or pinch
Reset viewDouble-click empty space

Trajectories and Playback

Multi-frame files, optimization paths, and scan results all load into the same playback view. Use the frame slider and play controls to step through them.

When a calculation result includes a plot (like a scan energy profile), the viewer and the plot stay synchronized — clicking a point on the plot jumps the viewer to that frame.