# The LabCanvas Protein viewer: PDB structures styled for figures

> How to show a protein structure in the LabCanvas Protein viewer: load any PDB ID or your own PDB and mmCIF file, choose cartoon, surface or ball-and-stick, colour by chain or secondary structure, select residues on the sequence and snapshot a transparent PNG for your figure.

Published 2026-10-18 by LabCanvas team. https://www.labcanvas.com/blog/protein-viewer-pdb-structures

![The LabCanvas Protein viewer showing a protein structure as a cartoon coloured by chain, with the sequence bar along the top](https://www.labcanvas.com/shots/protein.webp)

The **LabCanvas Protein viewer** is a focused viewer for protein structures. Load any entry of the RCSB Protein Data Bank by its ID, or your own PDB or mmCIF file, choose a style and a colouring, select residues on the sequence to give them their own look, and snapshot a transparent PNG straight into your figure.

## What it is for

- **Structure panels in papers**: a cartoon coloured by chain with the active site in ball-and-stick.
- **Predicted models** coloured by confidence (AlphaFold writes pLDDT into the B-factor column), next to the PAE plot made in [Graphs & statistics](https://www.labcanvas.com/blog/graphs-statistics-scientific-plots).
- **Teaching figures** of secondary structure, domains and binding sites.

## Styles and colourings

| Option | Choices |
| --- | --- |
| Representation | Cartoon, tube, trace, ball-and-stick, sticks, space-filling, lines, quick, solvent-excluded and solvent-accessible surfaces |
| Colouring | Secondary structure, chain, rainbow (N → C), element, residue type, hydrophobicity, B-factor or one colour |
| Materials | Soft, glossy, metal, toon or flat |
| Selection | Residues picked on the sequence bar get their own style and colour |
| Output | Transparent PNG snapshot into a figure, slide or poster |

## How to show a protein and highlight residues

1. Open the [Protein viewer](https://www.labcanvas.com/protein.html) and enter a PDB ID such as **4HHB**.
2. Pick a style and colouring, for example cartoon by chain.
3. Drag across residues on the sequence bar to select them.
4. Give the selection its own style (ball-and-stick) and colour.
5. Turn the view, then take a snapshot and add it to your figure.

## Protein figures made in LabCanvas

The template library includes graphical abstracts of protein structure prediction, built from protein objects, confidence plots and diagrams you can edit.

:::grid
![AlphaFold: a predicted structure and how sure it is: an editable graphical abstract template](https://www.labcanvas.com/templates/alphafold-predicted-structure-confidence.webp "AlphaFold: a predicted structure and how sure it is")
![Inside AlphaFold 2 and AlphaFold 3: an editable graphical abstract template](https://www.labcanvas.com/templates/alphafold-2-and-3-architecture.webp "Inside AlphaFold 2 and AlphaFold 3")
![Protein folding: the energy landscape: an editable graphical abstract template](https://www.labcanvas.com/templates/protein-folding-energy-landscape.webp "Protein folding: the energy landscape")
:::

## Frequently asked questions

### Which structures can I open?

Any entry of the RCSB Protein Data Bank by its four-character ID (for example 4HHB for haemoglobin), or your own PDB or mmCIF file, including predicted models such as AlphaFold structures.

### Which styles and colourings are there?

Cartoon, tube, trace, ball-and-stick, sticks, space-filling, lines and three kinds of surface, coloured by secondary structure, chain, rainbow (N → C), element, residue type, hydrophobicity, B-factor or one colour. AlphaFold models store pLDDT in the B-factor column, so B-factor colouring shows their confidence.

### How do I highlight a binding site?

Drag across residues on the sequence bar to select them, then give the selection its own style and colour, for example ball-and-stick in orange over a grey cartoon.

### How do I put the protein in a figure?

Take a snapshot: it is a transparent PNG that goes straight into your figure, slide or poster, where you can label it with the figure tools.

### What powers the viewer?

The Protein viewer is built on Miew, an open-source molecular viewer, inside the LabCanvas interface.

## Related links

- [Open the Protein viewer](https://www.labcanvas.com/protein.html)
- [AlphaFold and protein templates](https://www.labcanvas.com/templates): Graphical abstracts of structure prediction
- [Graphs for proteins](https://www.labcanvas.com/blog/graphs-statistics-scientific-plots#proteins-drug-discovery): PAE, pLDDT, contact maps and Ramachandran plots
- [3D Studio guide](https://www.labcanvas.com/blog/3d-studio-scientific-3d-models)
- [Show a protein: tutorial](https://www.labcanvas.com/tutorials)