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    <pre><code>import numpy as np from math import * from pylab import * from matplotlib import pyplot as plt from matplotlib import animation # Constants isqrt = 2**(-0.5) omega = np.sqrt(2-np.sqrt(2)) #Angular velocity L=4 #Length of the system n = 1 #Normal mode number if n==1: z = [isqrt,1,isqrt] #mode 1 elif n==2: z = [1,0,-1] #mode 2 elif n==3: z = [isqrt,-1,isqrt] #mode 3 ex = [1,2,3] #x-coordinates of scatter points # First set up the figure, the axis, and the plot element we want to animate fig = plt.figure() ax = plt.axes(xlim=(0, L), ylim=(-1.1, 1.1)) line, = ax.plot([], [], lw=2, color='b') scat, = ax.plot([],[], linestyle='', marker='o', color='b') # initialization function: plot the background of each frame def init(): line.set_data([], []) scat.set_data([], []) return [scat,line,] # animation function. This is called sequentially def animate(t): xinterval = np.arange(0,10,0.05) wave = np.cos(0.1*omega*t)*np.sin(n*xinterval*np.pi/L) line.set_data(xinterval, wave) dots = z*real(np.exp(0+(omega*0.1*t)*1j)) scat.set_data(ex, dots) return [scat,line,] # call the animator. anim = animation.FuncAnimation(fig, animate,init_func=init, frames=range(200), interval=20, blit=True) plt.grid(True) plt.show() </code></pre> <p>Unless you have a complelling reason to use <code>scatter</code> (which is you want each marker to be a different color or size, which your example code does not show) the above will generate the same animation much more efficiently.</p> <p>The issue with your original code is that you are not updating the <code>scatter</code> artist each time through, you are adding a new artist which interacts with the blitting code in strange ways (on my machine, <em>all</em> of the previous dots randomly were visible or not).</p>
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    1. POFirst set of (scatter) plot data remains on the graph during animation with Python's matplotlib
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    1. POFirst set of (scatter) plot data remains on the graph during animation with Python's matplotlib
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    1. COThis is perfect, thank you! I'm happy to get rid of scatter, this looks much more cleaner.
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    2. CO@RobertK If this solved your problem, please accept it (the big gray check mark on the left)
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