First Visit: Explore Caffeine

Open Tako with a fresh local workspace and caffeine is ready in the viewer. The six-step Quick tour sits below the molecule so you can keep using the tools. It appears automatically once in this browser. Skip tour closes it; Minimize gives the viewer more room. Use Help → Tutorial mode to return to your saved step. Finishing the tour makes the next manual visit start at the beginning.

An existing workspace is preserved. Starting the tour manually adds or reopens its caffeine project. Shared links, demo links, and calculation handoffs open their intended work without an automatic tour. Tutorial progress is stored on this device and is separate from workspace files.

1. Look around

Drag empty space to rotate caffeine and scroll to zoom. On a touch screen, rotate with one finger and pinch with two fingers to zoom. Click or tap an atom to select it. The model contains 24 atoms, with formula C₈H₁₀N₄O₂, from the bundled PubChem conformer (CID 2519).

2. Find the editing tools

Add (＋) on the left brings in atoms or molecules from the library. Move (↔) changes the positions of selected atoms. Use Undo to reverse an experiment. You can leave caffeine unchanged for the first run; the tour always calculates the original isolated molecule.

3. Understand the method choices

MLIP means a machine-learned interatomic potential: use a model whose training domain covers your chemistry. Tight binding, including GFN2 and g-xTB, offers approximate electronic-structure calculations; this tour chooses GFN2. DFT provides density-functional calculations with options including PBE, r²SCAN, and SKALA. SKALA is a learned exchange–correlation functional within DFT. These families involve different cost and applicability tradeoffs; their order does not guarantee accuracy.

4. Run one small calculation

Press Run GFN2 in the tour. This explicitly starts a Single Point calculation of energy and forces: atoms stay at their input positions. It runs locally on your device and may download the calculation engine on its first run. Nothing starts merely because you opened the tour. Skip run continues immediately; Stop calculation cancels a running example.

For your own work, use Calculate → Single Point and select the method and properties in the setup dialog. Optimization and molecular dynamics are separate tasks in the same Calculate menu.

5. Read the result

The guide displays energy in electronvolts only after a completed run supplies a finite, converged result. A canceled or failed run is labeled explicitly. The calculation has its own workspace tab and Explorer folder. Console shows the log, including download or execution errors. History records structure edits. The tour remains usable while a calculation is running.

A computed model energy is not a measured physical property. Compare energies with consistent methods and compositions; use a scientifically appropriate reference and validation for predictions.

6. Keep your work and go further

Tako saves the workspace in this browser when storage is available. File → Export Workspace ZIP makes a portable backup, and File → Open can restore that archive. Export important work before clearing browser data or changing devices.

Try geometry optimization to relax atomic positions, then molecular dynamics to follow motion over time. Molecular vibrations introduces spectra. Agent, notebooks, and scripts support longer automated workflows; they are optional after this first tour.

On mobile, the first-run Explorer and Inspector stay hidden to leave space for the molecule. The guide fits below the viewer, moves beside it on short landscape screens, scrolls internally when necessary, and can be minimized. Toolbars scroll horizontally to preserve the model’s space. Use the guide’s Open Console action for execution details.

Structure provenance: PubChem caffeine, CID 2519. Method background: SKALA model documentation.