VMD-L Mailing List

From: Joshua A. Anderson (joaander_at_umich.edu)
Date: Mon Jun 27 2011 - 11:50:44 CDT

On Jun 27, 2011, at 10:55 AM, Brian Puchala wrote:

> I currently have a script that uploads data for each frame into "User" and colors using that. The data tells which atoms are grouped in a certain way which varies from frame to frame. I would like to give each group a distinct color. When there are more than about three or four different groups the color scale does not provide enough contrast between different groups, so I would like to be able to specify particular colors.

If you go under Graphics->Colors and select the color scale tab, you can change to a different color scale. Its been a while since I did this last, but I think the BGR color scale worked better than the default RWB. You can also fiddle with the offset and midpoint sliders to see if you can improve it at all.

> Is there an atom attribute that changes from frame to frame but does not use the color scale for coloring?

Not that I've found. The color by traj only lists user, time, and velocity. It would be nice to have an integer use field and a per time step coloring that worked like color by ResId (I abuse ResId quite a bit for single frames for this purpose). An alternate (possibly even more useful) hack would be a way to specify by hand the color scale. Then we can split the floating point 0-1 color scale into any number of subdomains and choose a color for each so that color by user will provide the desired effect.

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Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan