I usually use R for plotting and it works quite well. I am experimenting now a bit with 3d plots and found that R (using rgl and plot3d, points3d, etc.) gets a bit confused with really big data sets.

I thought that using software optimized for 3d visualization is a good idea for 3d plotting. By asking a few persons and a bit of googling I chose pymol as my experimental tool. And I feel pretty much in the middle of the sea.

Is there any suggestion on how I can transform a 3-column file into something readable and displayable (even just as dots will do) in pymol?

I've done this with the following format:

45
C 1 45 34
C -0.064 1.164 2.850
C 0.070 1.226 -2.713
C 0.018 2.765 1.316
C 0.081 2.792 -1.142

If files are small it works. Using Carbon as the atom will create a line plot as carbon can create bonds with carbons. If you use hydrogen (H) you will have a dot plot.

The problem is that my file is 3000000 lines long .... and it runs but MEGA sluggish

any suggestion to improve?