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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.

By LabCanvas team1 min read
The LabCanvas Protein viewer showing a protein structure as a cartoon coloured by chain, with the sequence bar along the top
Protein viewer in LabCanvas. Open it in your browser.
Contents

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.
  • Teaching figures of secondary structure, domains and binding sites.

Styles and colourings

OptionChoices
RepresentationCartoon, tube, trace, ball-and-stick, sticks, space-filling, lines, quick, solvent-excluded and solvent-accessible surfaces
ColouringSecondary structure, chain, rainbow (N → C), element, residue type, hydrophobicity, B-factor or one colour
MaterialsSoft, glossy, metal, toon or flat
SelectionResidues picked on the sequence bar get their own style and colour
OutputTransparent PNG snapshot into a figure, slide or poster

How to show a protein and highlight residues

  1. Open the Protein viewer 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.

AlphaFold: a predicted structure and how sure it is: an editable graphical abstract template
AlphaFold: a predicted structure and how sure it is
Inside AlphaFold 2 and AlphaFold 3: an editable graphical abstract template
Inside AlphaFold 2 and AlphaFold 3
Protein folding: the energy landscape: an editable graphical abstract template
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.
protein structurePDB viewermolecular visualizationstructural biologyAlphaFoldPyMOL alternative

Try it in LabCanvas

Every app is free to start in your browser. Create an account and begin.

Open Protein viewer