Animating spectra

The plot recipes defined within NMRTools provide an easy way to generate animations of spectral data, using the @animate macro defined within the Plots package. 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 - showing the progressive phosphorylation of cJun by JNK1 kinase. Read more about the paper here: Waudby et al. Nat Commun (2022).

using NMRTools, Plots

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 the Plots @animate macro, then saving as an animated gif.

anim = @animate for i=1:nt
    # generate a nice title with the time rounded to 1 decimal place, e.g. "Time elapsed: 0.1 hr"
    titletext = "Time elapsed: $(round(thr[i],digits=1)) hr"
    plot(spec[:,:,i], title=titletext)
end

# save as an animated gif
gif(anim, "kinetics.gif", fps=30)

[ Info: Saved animation to /Users/runner/work/NMRTools.jl/NMRTools.jl/docs/build/kinetics.gif

2D titration

First, load in some data - as described in the tutorial on plotting.

spectra2d = exampledata("2D_HN_titration")

 Downloading artifact: 2D_HN_titration

Now loop over the spectra to produce the animation:

anim=@animate for spec in spectra2d
    plot(spec, xlims=(6,10.5), title=label(spec))
end

gif(anim, "titration.gif", fps=8)

[ Info: Saved animation to /Users/runner/work/NMRTools.jl/NMRTools.jl/docs/build/titration.gif

Note that spectra have been normalised automatically to account for differences in their number of scans or receiver gain.