PDB 3D model viewer

The RCSB Protein Data Bank holds experimentally determined (and some predicted) macromolecular structures. You need a 3D view when you are checking whether a mutation sits on the surface, comparing two published structures, teaching a student what a kinase domain looks like, or simply checking a homology model before you order DNA.

We use this page for quick looks without installing PyMOL or ChimeraX on every machine in the lab. Typical jobs might include opening the structure described in a paper figure, inspecting an interface between two chains, highlighting a ligand-binding pocket in stick mode, or flipping through frames from an MD export that you have made in GROMACS. It is a visualisation aid, not structure determination, docking, or energy minimisation.

For publication-quality figures or measurements (distances, angles, electrostatics), use dedicated software. For sequence-level work on the same project, pair this viewer with our restriction digest analyser or DNA reverse & complement tools on the cloning side.

Rendering uses 3Dmol.js in your browser. When you enter a PDB ID and click Load, the page requests the coordinate file from files.rcsb.org. Keyword search calls the public RCSB Search API and lists matching entry IDs. You can open any hit in the viewer or jump to the official RCSB structure page.

Local files are read with the File API on your device only. They are not uploaded to thebondlab.net. After parsing, the viewer detects chain identifiers from ATOM / HETATM records and builds a colour picker per chain. Changing the Style dropdown redraws the scene (cartoon uses a rainbow spectrum when no custom chain colours are set).

Multi-model PDBs contain several MODEL … ENDMDL blocks (common for MD trajectories). The tool counts models on load and enables Play / Pause / Stop with loop modes (forward, backward, back-and-forth) and a frame interval slider. Single-model structures show “Single model (no animation)” in the animation panel.

Display options

• Cartoon. Secondary-structure ribbons. A good default for proteins.
• Stick. Bonds drawn as sticks. Useful for small sites and ligands.
• Line. Minimal wireframe for dense structures.
• Sphere. CPK-style spheres (can be heavy on large structures).
• Surface + stick. Van der Waals surface with sticks underneath for context.

1. By PDB ID: type a four-character ID (e.g. 1CRN crambin, 1BNA B-DNA, 7K00 spike fragment) and click Load. The page loads 1CRN on first visit as a demo.
2. By search: enter a protein or complex name (e.g. hemoglobin, p53 DNA binding, kinase) and click Search RCSB. Pick Open in viewer or open the RCSB entry in a new tab for metadata and citations.
3. From disk: choose a .pdb or .ent file and click Load local PDB. Use this for MD snapshots, AlphaFold exports saved as PDB, or files too new to appear in RCSB yet.
4. Navigate: drag to rotate, scroll or pinch to zoom, use Reset view if you get lost. Change Style any time; chain colours update live.
5. Chains: under Chain colors, pick a colour per chain (handy for heterodimers). Reset chain colors restores the default palette.
6. Animation: if the status line reports multiple models, set speed and loop mode, then Play. Stop returns to frame 1.

Tip: large structures and Surface + stick can be slow on older laptops. Start with cartoon, then switch to stick for the region you care about.

• PDB format only here. mmCIF / BinaryCIF from RCSB are not loaded by this page; convert or download legacy PDB if needed.
• ID fetch = RCSB PDB file. Very large entries may be slow or hit browser memory limits; try a biological assembly or a trimmed export from RCSB if load fails.
• No measurements or editing. No distance picks, mutagenesis, or file export from the viewer.
• Hydrogens and alt locs are shown as in the file; we do not clean or protonate structures.
• Network for IDs and search. Loading by ID or searching sends requests to RCSB servers (see their privacy terms). Local files do not leave your machine.
• Third-party script. 3Dmol.js is loaded from 3Dmol.org; if that CDN is blocked, the viewer will not start.

• Restriction digest analyser — map cut sites when planning cloning after inspecting a construct.
• Promoter Grabber — fetch promoter sequence for motif or reporter work on the same gene.
• TF binding scanner — scan DNA for motif hits once you have sequence.
• Molecular biology guides — method notes including western blot and qPCR topics from our lab.