Getting Started
This tutorial walks you through loading your first crystal structure in CatGo, exploring the 3D viewer, and exporting the result.
Loading a Structure
CatGo supports several ways to load structures:
Drag and Drop
The simplest method — drag a structure file (.cif, .poscar, .xyz, .extxyz, .json) directly onto the 3D viewer. Compressed files (.gz, .zip) are also supported.
File Picker
Click the Import button in the toolbar to open a file browser dialog.
Paste Content
Click the Paste button (or use the paste icon in the toolbar) to open a text modal. Paste CIF, POSCAR, or XYZ content directly and press Ctrl+Enter (or Cmd+Enter on macOS) to import.
Database Search
Use the OPTIMADE or PubChem search modals to find structures from online databases. See the Database Search tutorial for details.
Navigating the 3D Viewer
Once a structure is loaded, you can interact with it using the mouse and keyboard:
Mouse Controls
| Action | Control |
|---|---|
| Rotate | Left-click and drag |
| Roll | Right-click and drag |
| Zoom | Scroll wheel |
| Pan | Shift + drag (or Ctrl/Cmd + drag) |
Keyboard Controls
| Key | Action |
|---|---|
| Arrow keys | Rotate structure (pitch and yaw) |
| W / S | Roll structure |
| R | Reset camera to default view |
| F | Toggle fullscreen |
| I | Toggle info pane |
| Escape | Close open panes / exit editing modes |
Selecting Atoms
- Click an atom to select it — the info pane shows its element, index, and coordinates.
- Shift+click to add/remove atoms from the selection.
- Double-click the background to clear the selection.
- Delete or Backspace removes selected atoms from the structure.
Toggling Display Options
Use the Controls panel (gear icon) to adjust the viewer:
| Option | Description |
|---|---|
| Show Bonds | Toggle bond display |
| Show Cell | Display unit cell wireframe |
| Show Image Atoms | Show PBC image atoms on cell edges |
| Show Labels | Element symbols on atoms |
| Camera Projection | Switch between perspective and orthographic |
| Color Scheme | Choose from Vesta, Jmol, Alloy, Pastel, Muted, Dark Mode |
| Atom Radius | Adjust sphere size |
| Depth Cueing | Add fog effect for depth perception |
Inspecting Structure Properties
Press I or click the info icon to open the Info Pane, which shows:
- Chemical formula and composition
- Space group and crystal system (via Spglib/Moyo)
- Lattice parameters (a, b, c, alpha, beta, gamma)
- Cell volume and density
- Number of sites
Exporting
Click the Export button in the toolbar to save the structure:
| Format | Extension | Use Case |
|---|---|---|
| CIF | .cif | Standard crystallographic exchange |
| POSCAR | .poscar | VASP input files |
| XYZ | .xyz | Simple Cartesian coordinates |
| Extended XYZ | .extxyz | XYZ with lattice and properties |
| JSON | .json | Pymatgen-compatible JSON |
| GLB | .glb | 3D model for presentations |
| OBJ | .obj | 3D model for rendering software |
Undo / Redo
All structure modifications (adding/deleting/moving atoms, slab cuts, supercells) support undo and redo:
- Ctrl+Z (Cmd+Z on macOS) — Undo
- Ctrl+Shift+Z (Cmd+Shift+Z on macOS) — Redo
Next Steps
- Building Slabs — Generate surface slabs from Miller indices
- Running an Optimization — Relax structures with ML potentials
- Searching Databases — Find structures from OPTIMADE, Materials Project, and PubChem