ProtPlot

ProtPlot is a Julia package for rendering 3D protein ribbon and other miscellaneous protein-related plots using Makie.jl.

Examples

Ribbon plots are constructed from vectors of protein backbones represented as 3x3xL arrays. For convenience, argument conversion methods are defined, and the ribbon constructors can take:

• a 3x3xL array of residue backbone atom coordinates (N, Ca, C), or a vector of these for each chain.
• a BioStructures.MolecularStructure or BioStructures.Chain.
• 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)

Customizing colors

Use the colors keyword argument to customize colors at the residue level. This argument should be a vector of vectors, where each vector contains either:

• values between 0 and 1, representing the colors of each residue in their respective chains according to the colormap.
• a list of Colorants, one per residue. For example, RGBA(1, 0, 0, 0.5) for a 50% transparent red. Load the ColorTypes or Colors package to create such Colorants.

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

colors = rand.(length.(chains))

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

Chains can be colored by chain using something like:

colormap = [:royalblue, :violet, :limegreen, :chocolate1]
colors = [fill(i-1, l) / (length(colormap)-1) for (i, l) in enumerate(length.(struc))]
ribbon!(scene, chains; colors, colormap)

and then you might get something like:

Camera controls

Makie allows programmatic control over the camera. Use the camcontrols keyword to control the initial view in a ribbon_scene call:

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

See also

• BioMakie.jl (designed for more interactivity)