From: Leonor Cruzeiro (
Date: Mon Apr 04 2005 - 11:22:02 CDT

Dear All,

I am a recent user of VMD, which I find really good and generally easy to use. But I have been trying to do a specific coloring in an animation and have not succeeded. I send attached a script (adapted from another that John Stone has sent to several people) to try and do what I want, but which does not quite work. The main problem is that I do not really understand how to "populate user fields". What I would like to have is a script that, for each frame, selects a few atoms in a specified residue and colors those in yellow, without changing the colors of the rest of the molecule. The script below does almost that, but atoms in the sidechain don't get colored differently and those that do show up in a different color in each timestep do not have the color I would like them to have, that is, yellow.

I would be very grateful if somebody could tell me what is wrong with my script and how I can change it to do exactly what I want.

Thanking you in advance,

Best wishes,
Leonor Cruzeiro.