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Ribbon

Interactive scene

using GLMakie, ProtPlot
using ProteinChains

ribbon(pdb"1ASS")
Example block output
ribbon(pdb"1ASS", colors=rand.(length.(pdb"1ASS")))
Example block output

Add to existing scene

fig = Figure()
ax = LScene(fig[1,1])

ribbon!(ax, get_backbone(pdb"1EYE"A))
ribbon!(ax, get_backbone(pdb"1EYE"A) .+ [-30, 30, 0], colormap=:blues)

fig
Example block output

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)

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

ribbon(pdb"1ASS",
    coil_diameter=0.6, helix_width=1.5,
    strand_width=1.5, strand_arrow_head_length=3.0)
Example block output

Animation

Ribbon plots are rendered as a set of surfaces, but observables don't properly propagate the updates since the number of surfaces may vary, unlike other plot types, which can render everything in a single Makie call. For animating ribbon plots, one solution is to delete the plot from the scene and redraw it every frame.

fig = Figure()
ax = LScene(fig[1,1])

p = ribbon!(ax, pdb"1ASS")

delete!(ax.scene, p)

ribbon!(ax, pdb"1EYE")

fig
Example block output

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