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Molecule

Proteins and small molecules in 3D, wired to your own notes.

Molecule ships 222 structures inside the cartridge: 105 experimental structures from the PDB and 117 small molecules from ChEBI. It reaches no network. Every structure carries stable identifiers: a PDB ID such as 1HHO, a UniProt accession such as P69905, a ChEBI ID, an InChIKey. Notes that say "haemoglobin", 1HHO or P69905 all lead to the same molecule.

The cartridge id is @mnemosyne-plugins/mnemo-molecule. Its code lives at Mnemosyne-OS/MnemoMolecule.

The library​

Type in Search a structure, an id, a formula…. Filter with All, Experimental structures or Small molecules, and with families such as Enzymes, Hormones, Sugars or Molecular machines. Click a row to put the structure on the stage.

The library says what it is: a chosen slice of the PDB and ChEBI. The reason for each entry shows under Why it is here.

The identity card​

A PDB entry is one experiment, not the protein. The card shows both, named:

  • This experiment: Method, Resolution, Released, Atoms, Chains, Organism.
  • The protein: its UniProt accession.
  • For a small molecule, The compound: Formula, Mass, Charge, InChIKey.

A resolution nobody reported shows a dash. A coarse resolution gets a sentence, because a 3.5 Å structure and a 1 Å structure look the same on screen.

The stage​

Draw the structure as Cartoon, Sticks, Spheres or Surface. Spin turns it by itself. Recentre brings back the start. A large structure, such as the 80S ribosome, takes a while to load and says so.

Ask your memory​

Press Ask what my notes say. It runs a model over your own vaults, so it costs an inference on a cloud route. Nothing is asked until you press it.

Review​

Quiz me opens the review. Pick a family, then a length, or Until I stop. Each question shows a structure and asks Which one is this?. At the end, Write this session to my memory writes the run into Molecule's own vault.

Hand gestures​

With hand tracking on and the window full screen, Molecule takes orbit, depth, zoom and recenter. Pinch and move to turn the structure. You can teach a pose for Spin. The hand button lists the gestures and sets the turn and zoom speeds. The cartridge receives moves, never the camera image.

Where your data goes​

  • The structures ship with the cartridge and are read from your disk.
  • Your review progress and gesture speeds are kept by Mnemosyne OS as the cartridge's saved state.
  • A review run reaches memory only when you press the save button. It lands in Molecule's own vault, walled off until you make it permanent.

Data sources and licences, as listed in the cartridge:

  • Experimental structures: RCSB PDB, CC0 1.0.
  • Small molecules: ChEBI (EMBL-EBI), CC BY 4.0.
  • 3D viewer: 3Dmol.js, BSD 3-Clause.

For agents​

ActionEffectWhat it does
statusreadThe structure on stage, its drawing, spin and library filter.
findreadLibrary entries matching a text, a kind or a family.
showwritePuts a structure on the stage.
setStylewriteCartoon, sticks, spheres or surface.
spinwriteStarts or stops the spin.
resetViewwriteBack to the starting angle and size.
filterLibrarywriteFilters the library list.
zoom, turnwriteMoves the structure, as the hands do.
showRandomwriteA random structure, optionally of one kind or family.
showPanel, closePanelwriteThe review or the gestures panel.

Voice examples: "show caffeine", "show insulin as sticks", "make it spin", "show me a random sugar", "quiz me".