I'm sorry for bothering all of you so often these past few days... but I ran into another issue. I opened a pdb and corresponding trajectory .nc file, and I ran "mlp #1 key true". Lipophilicity coloring showed up, but when I played the trajectory, the mpl colors went away and the default colors came back. I noticed the same happened for "coulombic" command. For now, I'm making due with a custom attribute file and "color byattribute name palette lipophilicity" from this tutorial https://www.cgl.ucsf.edu/chimerax/docs/user/formats/defattr.html#examples. It does stay throughout the trajectory but doesn't look as good, and the colors aren't blended.

I have also tried doing "mlp map true" and "color sample #1 map #2" with #1 being the pdb with trajectory and #2 the resulting map from mlp. It looked really bad. The protein is now one color. 

"mlp map true" command