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ProtPlot

Latest Release MIT license Build Status Coverage

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

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)

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 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)

random colors

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{Int} where 1 means loop, 2 means helix, and 3 means strand)

  • 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)))

camera