We have had a number of problems with this, two of which I have attempted to solve in #1070 and #1073. I think the problem is that this function is a bit of a hybrid of plt.scatter and plt.plot with some custom things that don't make a lot of sense and may have got broken easily as a consequence. This may also be due to differences between the 2D and 3D versions of these functions.
It could be useful to look at the blame on this file (https://github.com/prody/ProDy/blame/master/prody/dynamics/plotting.py) and work out what changed when and why.
Here's an early version of the code using plt.plot for 2D and mpl_toolkits.mplot3d.Axes3D.plot for 3D, which very clean and simple using matplotlib to handle everything. Obviously, there are reasons for changes since this point, but it looks like a good model to strive for.
7023d3a#diff-766762f87f6dc7009128d2551201a6e3
We have had a number of problems with this, two of which I have attempted to solve in #1070 and #1073. I think the problem is that this function is a bit of a hybrid of plt.scatter and plt.plot with some custom things that don't make a lot of sense and may have got broken easily as a consequence. This may also be due to differences between the 2D and 3D versions of these functions.
It could be useful to look at the blame on this file (https://github.com/prody/ProDy/blame/master/prody/dynamics/plotting.py) and work out what changed when and why.
Here's an early version of the code using plt.plot for 2D and mpl_toolkits.mplot3d.Axes3D.plot for 3D, which very clean and simple using matplotlib to handle everything. Obviously, there are reasons for changes since this point, but it looks like a good model to strive for.
7023d3a#diff-766762f87f6dc7009128d2551201a6e3