How to Explore a Protein Structure with the Free MolDraw Protein Viewer
Short answer: Open the Protein Viewer, type a four-character PDB ID and press Load PDB ID, or press Upload PDB file. Pick a Default Chain Style, then style each chain in the Chains list. Drag across the Amino Acid Sequence and right-click to restyle or hide that stretch. Save the view as PNG or JPG, or the coordinates as PDB, XYZ, OBJ or X3D.
Try the protein viewer here
The live viewer below is the same tool as the full page. It loads crambin (1CRN) when it opens.
Why use a protein viewer in the browser?
A protein's function depends on its 3D shape. Desktop programs such as PyMOL or ChimeraX are powerful, but you need to install them and learn their commands. For a quick look, a class demonstration or a simple figure, a web page is often enough.
This page is the standalone web tool. MolDraw also has a Protein viewer plugin inside the editor. The plugin sits next to your drawing and adds more colour schemes, molecular surfaces and extra export formats. The standalone page is lighter and opens without the editor.
Protein structures in brief
The Protein Data Bank (PDB) is the public archive of experimentally determined structures of proteins, nucleic acids and their complexes. Most come from X-ray crystallography, NMR or cryo-electron microscopy. Each entry has a four-character ID, such as 1CRN for crambin or 4HHB for human deoxyhaemoglobin.
An entry lists atom coordinates. Atoms belong to residues, the amino acids, which are numbered along each chain. Chains have letter IDs (A, B, C and so on). Haemoglobin, for example, has two α and two β chains. Ligands, ions and water are stored as separate hetero atoms. Parts of a chain that were not resolved in the experiment are simply missing from the model.
Each display style answers a different question. A cartoon traces the backbone and shows helices and β-strands, so you see the overall fold. Sticks show bonds between atoms, which you need for side chains and binding contacts. Spheres fill space and show packing. A surface shows the outer shape and pockets; this page does not draw surfaces, but the in-editor plugin does.
Input and export formats
| Load | A PDB ID, downloaded from RCSB in PDB format, or a .pdb file from your computer. |
|---|---|
| PNG and JPG | An image of the current view. JPG gets a white background. |
| PDB | The loaded file as it was read. |
| XYZ | The element and coordinates of every atom, including hetero atoms. |
| OBJ and X3D | Simple point-based models of the atom positions. They do not copy the cartoon or the styles on screen. |
How to explore a structure step by step
- Open the viewer. Crambin (1CRN) loads first, so you can try the controls straight away.
- Type an ID in PDB ID, for example 4HHB, and press Load PDB ID. The status line lists the chains it found. To open your own file, press Upload PDB file.
- Choose Cartoon, Stick, Sphere or Line in Default Chain Style. This sets every chain at once.
- Drag in the 3D view to rotate the molecule, and scroll to zoom.
- In Chains, each chain shows its residue count, a style menu, a colour picker and a Hide box. Press Focus to highlight that chain in orange sticks.
- In Amino Acid Sequence, drag across residues in one chain. Right-click the selection to open Selected Segment Style, set Style, Color or Hide segment, and press Apply.
- Use the download buttons to save your result. Clear empties the viewer.
What the viewer does
- Per-chain styles: give each chain its own style and colour, or hide it, to see how subunits pack.
- Sequence view: one-letter codes for each chain, linked to the 3D model.
- Segment styles: restyle, recolour or hide a selected stretch of residues. Each applied segment keeps its own style, so you can mark several sites.
- Downloads: PNG, JPG, PDB, XYZ, OBJ and X3D.
Ways to use it in class and in the lab
- Teaching quaternary structure: load 4HHB, give each chain a different colour and hide one or two chains to show how the subunits fit together.
- Highlighting a site: keep the protein as a cartoon and show a binding loop or a mutation site as coloured sticks.
- Quick figures: set up a view and download a PNG for a slide or a report.
- Next steps: turn a bound ligand into SMILES with PDB to SMILES, work out a chain's mass with the protein molecular weight calculator, or prepare a receptor with PDB to PDBQT.
Tips and limits
- Cartoon draws only the backbone trace of the chains, not ligands, ions or water. To see them, switch the chain to Stick, Sphere or Line.
- For large structures, Line is the lightest style.
- The sequence comes from the residues in the model. Unresolved residues do not appear, and residues the viewer does not recognise, such as nucleotides, show as X.
- A selection stays within one chain. Sequence selection uses drag and right-click, so a mouse is easiest.
- Loading by ID needs an internet connection.
Want surfaces, more colour schemes or GLB export? Use the Protein viewer plugin in the MolDraw editor.
Questions and answers
How is this page different from the Protein plugin in the MolDraw editor?
This page is a light, standalone viewer that opens without the editor. The Protein plugin sits next to your drawing in the editor and adds more colour schemes, molecular surfaces and extra export formats such as GLB and SDF.
Where do the structures come from?
When you press Load PDB ID, the page downloads the entry from the RCSB Protein Data Bank, so you need an internet connection. With Upload PDB file, the page reads the file in your browser.
Why can I not see the ligand or the water molecules?
Cartoon draws only the backbone trace of the chains. Set the chain to Stick, Sphere or Line in the Chains list to see ligands, ions and water as atoms.
Can I open mmCIF files?
No. The page reads the PDB format only. Most entries can be downloaded as a .pdb file from RCSB, but some very large structures are only offered as mmCIF. Those will not load here.