From: John Stone (
Date: Wed Apr 06 2005 - 13:49:01 CDT

  Your script looks pretty reasonable, but your explanation isn't
entirely clear to me. You said "atoms in the sidechain don't get
colored differently". Differently than what? The atoms for which no
value is set, or non-sidechain atoms in the same residue? Which frames
does this occur in? Your script uses slightly different atom selections
for a couple of frames. The mapping of "user" value to colors is controlled
by the "color scale data range" setting in the "Trajectory" tab of the
graphical representations window. If you've left this set to auto, then
the active VMD color scale will be applied over the entire range of data
values from min to max. If you want a particular range to be selected, you
can manually set this. The "mol scaleminmax" command at the end of my
original script was forcing this to "auto" by setting min/max values of zero.
You can set this to a range that's appropriate for your data (for all frames)
and then you will get the colors you expect.

  John Stone

On Mon, Apr 04, 2005 at 05:22:02PM +0100, Leonor Cruzeiro wrote:
> 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.

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