Molecules in 3D

Open a structure.
See where it came from.

Ask SynapseX Chat for a protein, a small molecule or a crystal and it opens in 3D inside the conversation: fetched from the public database, cleaned, and labelled with its source. The numbers on the card are computed from the file, never written by the model.

Open SynapseX ChatSee all visualizations
3proteins, small molecules, crystals
4public sources: PDB, AlphaFold DB, PubChem, COD
24residues highlighted at once
Ådistances computed from the file
3proteins, small molecules, crystals
4public sources: PDB, AlphaFold DB, PubChem, COD
24residues highlighted at once
Ådistances computed from the file
3proteins, small molecules, crystals
4public sources: PDB, AlphaFold DB, PubChem, COD
24residues highlighted at once
Ådistances computed from the file
What you can open

Name it, or paste it.
It opens in the conversation.

Ask for a structure by its public identifier and SynapseX fetches it from the source database. The card appears in the conversation and is listed with its outputs.

Proteins

From

A PDB ID from the Protein Data Bank, a UniProt ID for the precomputed AlphaFold DB model, or PDB text you paste.

The card reports

Chains, ligands, and metal sites with their coordinating atoms.

Small molecules

From

A PubChem name or CID, or MOL/SDF you paste. A 3D conformer when PubChem has one, otherwise the 2D layout — and the card says which.

The card reports

Hill formula, molar mass, heavy-atom and bond counts, net formal charge.

Crystals

From

A COD ID from the Crystallography Open Database, or CIF text you paste.

The card reports

Cell volume, the symmetry-expanded formula, cell weight, and density when Z is given.

Where it came from

Measured, predicted,
or yours. Never blurred.

A predicted model and an experimental structure look alike in 3D. Every protein card says which one you are looking at, so the picture cannot carry more confidence than its source.

  1. experimental structureDeposited in the Protein Data Bank and fetched by its PDB ID.
  2. predicted modelPrecomputed in AlphaFold DB, fetched by UniProt ID, and coloured by its pLDDT confidence.
  3. provided coordinatesText you pasted. SynapseX shows it, and says its origin is unverified.
On the card

Look closely.
Measure from the file.

Switch style and colouring, frame a ligand or a metal site, and highlight the residues the conversation is about. What the card reports comes from the coordinates, not from the language model.

cartoonstickssurfacespherespLDDT

Styles and colours

Cartoon, sticks, surface or spheres; colour by spectrum, chain, secondary structure, element, or pLDDT for predicted models.

Focus

Frame the whole structure, the ligand, a metal site, or up to 24 highlighted residues. Labels toggle on and off.

Cleaned, and it says so

Waters and common additives removed, alternate locations collapsed, extra models dropped, with the counts on the card.

Computed, not generated

Distances in ångström to two decimals, formulas and masses come from the file through a parser.

What it does not do

A viewer,
not a predictor.

  • No structure prediction, folding or docking.
  • No superposition or side-by-side comparison of two structures.
  • No annotations you click onto the model.
  • The camera and style you choose are not saved with the card.
  • Not read: mmCIF, MOL2, XYZ, POSCAR.
FAQ

What people ask
before they trust a picture.

Proteins and nucleic acids from the Protein Data Bank by PDB ID, AlphaFold models by UniProt ID, small molecules from PubChem by name or CID, and crystals from the Crystallography Open Database by COD ID. You can also paste the structure text yourself: PDB for proteins, MOL or SDF for molecules, CIF for crystals.

No. SynapseX shows structures; it does not predict, fold or dock them. An AlphaFold model is fetched precomputed from the AlphaFold Database, and the card labels it a predicted model and colours it by its confidence score.

Every protein card says which of three it is: an experimental structure from the PDB, a predicted model from AlphaFold DB, or coordinates you supplied, whose origin SynapseX cannot verify. Small molecules from PubChem say whether you are looking at a 3D conformer or a flat 2D layout.

Computed. Formulas, masses, atom counts, cell volumes and distances are read from the structure file by a parser, never written by the language model. The card also says what was cleaned before display, such as waters and common additives removed.

Each structure card stays in the conversation and is listed under its outputs, so you can find it again. Conversations in SynapseX Labs live in a workspace with the rest of the project.

Not yet. A card shows one structure from one source. Superposing or comparing structures side by side is not something SynapseX offers today.

Name a protein.
See it in the chat.

Ask for a PDB ID, a UniProt ID, a PubChem compound or a COD crystal, and the structure opens in the conversation with its source on the card.

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