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How to view a protein from the PDB or AlphaFold

Choose Open a protein structure (press Ctrl+K and type it), or type the id into Quick insert, and enter a PDB id such as 1CRN or a UniProt accession for an AlphaFold model. It opens in the 3D preview as a ribbon, and Cite gives the reference.

Needs an internet connectionOn a Mac, Ctrl is Cmd.

Steps

  1. Press Ctrl+K, type Open a protein structure, and press Enter.

  2. Type the entry and press Open:

    • a PDB id such as 1CRN or 1UBQ for an experimental structure from the RCSB Protein Data Bank, or
    • a UniProt accession such as P69905 for an AlphaFold model.

    The Open a protein structure dialog with 1CRN typed in.The Open a protein structure dialog with 1CRN typed in.

  3. The protein opens in the 3D preview panel as a ribbon, colored by its secondary structure. Under it are the entry's title, how many residues and chains it has, and where it came from. Drag to turn it.

    Crambin (PDB 1CRN) in the 3D preview: a ribbon colored by structure, the entry's title and size, Surface, and Cite PDB 1CRN.Crambin (PDB 1CRN) in the 3D preview: a ribbon colored by structure, the entry's title and size, Surface, and Cite PDB 1CRN.

Quicker: press / for Quick insert, type the PDB id, and choose Open protein 1CRN from the PDB.

In the 3D preview

Control Does
Color by structure How the ribbon is colored: by structure or by chain
Surface Off, or a surface colored by Hydropathy or by Element
Docking Browse docking poses in this protein from an SDF, MOL2 or PDBQT file
Story Narrated scenes over the structure, with a link you can send
AR / VR View it in AR or VR, or download the 3D model
Insert Puts a picture of the view on the canvas
Video Records one turn as a video
Close Closes the protein and goes back to the drawing

If the file has a ligand, the panel lists its contacts. Waters are not counted as ligands.

Cite the entry

Press Cite PDB 1CRN (the button names the entry). The citation card gives the entry's reference and the database's own paper in a style you choose, such as ACS.

The Cite card for 1CRN in ACS style: the entry's reference and the Protein Data Bank paper, Copy both, Add to document refs, BibTeX and RIS.The Cite card for 1CRN in ACS style: the entry's reference and the Protein Data Bank paper, Copy both, Add to document refs, BibTeX and RIS.

  • Copy both copies the two references.
  • Add to document refs adds them to the document's references.
  • BibTeX and RIS download them for Zotero, EndNote or Mendeley.

Note

Proteins come straight from the RCSB Protein Data Bank (files.rcsb.org) and the AlphaFold database (alphafold.ebi.ac.uk), so this needs a connection.

3D and orbitalsHow to view a structure in 3DSelect the structure and choose View › 3D view or press Shift+D. Drag to turn, shift-drag to pan, scroll to zoom. The 2D button in the top bar goes back.BiochemistryHow to build a peptide, DNA or RNA from its sequenceChoose Insert › Build from sequence…, type the one-letter sequence, pick Peptide, DNA or RNA and Residues or Full structure, and press Insert.Files and formatsReferencesThe References panel in Athanor keeps the document's numbered reference list in one citation style, ready to copy into a paper, a slide or a report.

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Last updated Nov 12, 2026