ProtPlot

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. For convenience, argument conversion methods are defined, so you can also pass:

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

Attributes

You may customize the geometry of the ribbon by specifying the value of attributes in the keyword arguments of your call. Here's a list of available attributes and their defaults:

• secondary_structures = nothing (gets assigned by an algorithm by default; needs to be a vector of Vector{Char} where '-' is loop, 'H' is helix, and 'E' is sheet)

• colors = nothing (gets assigned range(0, 1, L) for each chain by default, mapping to colormap; overrides colormap if colorants are given)

• colormap = :jet (see the ColorSchemes.jl catalogue; can also be a vector of colorants)

• coil_diameter = 0.4

• coil_spline_quality = 20

• coil_slice_quality = 20

• helix_width = 2.0

• helix_thickness = 0.5

• helix_spline_quality = 20

• helix_slice_quality = 20

• strand_width = 2.0

• strand_thickness = 0.5

• strand_arrow_head_length = 5.0

• strand_arrow_head_width = 3.5

• strand_spline_quality = 20

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)))