ProtPlot

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ProtPlot is a Julia package for rendering 3D protein ribbon using Makie.jl.

Overview

ProtPlot exports the Ribbon plot:

  • ribbon: makes a static render of the ribbon.
  • ribbon!: renders the ribbon plot within an existing container (e.g., Scene or Axis3).
  • ribbon_scene: creates an interactive Scene to render the ribbon.

Examples

A ribbon plot is constructed from a Vector{Backboner.Protein.Chain}, which you can obtain from a PDB file using the exported readpdb function. Alternatively, you can pass a single chain, or a PDB file path.

using GLMakie # use the GLMakie backend
using ProtPlot

# Create and display a ribbon plot in an interactive window
ribbon_scene("test/data/1ASS.pdb", backgroundcolor=:black, colormap=:jet)

plain gradient

Customizing colors

Use the colors keyword argument to customize colors at the residue level. This argument should be a vector of vectors, where each inner vector contains values between 0 and 1, representing the colors of each residue in a chain according to the colormap. These colors are recursively passed to the rendering functions, ensuring that each residue is colored appropriately.

# Load protein data from a PDB file
chains = readpdb("test/data/1ASS.pdb")

colors = rand.(length.(chains))

ribbon_scene(chains, colors=colors, colormap=:hsv)

random colors

Camera controls

Makie allows programmatic control over the camera. Use the camcontrols keyword to control the initial view:

ribbon_scene("test/data/1ASS.pdb", camcontrols=(; lookat=Vec3f(30, 0, 60), eyeposition=Vec3f(160, -75, 0), upvector=Vec3f(0, 0, 1)))

camera