Animating spectra

Makie's record function can create animations of spectral data, saving directly to GIF or video formats. A couple of examples are provided below.

Phosphorylation kinetics

First, load in some data. This pseudo-3D kinetic data — a series of 1H,15N SOFAST-HMQC spectra — shows the progressive phosphorylation of cJun by JNK1 kinase. Read more about the paper here: Waudby et al. Nat Commun (2022).

using NMRTools, CairoMakie

spec = exampledata("pseudo3D_kinetics")

 Downloading artifact: pseudo3D_kinetics

The data have been processed in Topspin using ftnd 3 and ftnd 2, so that the final dimension of the 3D represents the phosphorylation time. Each 2D plane took 2 minutes to acquire, and there was an initial delay of 4 min between adding the kinase and recording the first free induction decay. We need to calculate a list of times from this information, that we can use to label the animation:

# get number of time points
nt = size(spec, 3)

# calculate a list of measurement times
# experiment was recorded with 2 min per spectrum, plus initial dead-time of 4 min
tmin = LinRange(0, 2*(nt-1), nt) .+ 4
thr = tmin / 60

256-element LinRange{Float64, Int64}:
 0.0666667, 0.1, 0.133333, 0.166667, 0.2, …, 8.46667, 8.5, 8.53333, 8.56667

Now we can generate the animation, by looping over each point in the time series with Makie's record function, then saving as an animated gif.

ref = spec[:, :, 1]
fig, ax, _ = nmrplot(ref; normalize=ref)
record(fig, "kinetics.gif", 1:nt; framerate=30) do i
    empty!(ax)
    ax.title[] = "Time elapsed: $(round(thr[i], digits=1)) hr"
    nmrplot!(ax, spec[:, :, i]; normalize=ref)
end

2D titration

First, load in some data — a series of 1H,15N HSQC spectra from a titration experiment:

spectra2d = exampledata("2D_HN_titration")

 Downloading artifact: 2D_HN_titration

Now loop over the spectra to produce the animation:

ref = spectra2d[1]
fig, ax, _ = nmrplot(ref; normalize=ref, xlims=(6, 10.5))
record(fig, "titration.gif", spectra2d; framerate=8) do s
    empty!(ax)
    ax.title[] = label(s)
    nmrplot!(ax, s; normalize=ref)
end