VMD-L Mailing List

From: Joshua Anderson (joaander_at_umich.edu)
Date: Fri Apr 16 2010 - 12:25:47 CDT

On Apr 16, 2010, at 1:03 PM, Axel Kohlmeyer wrote:

> have you tried using coloring by "Element"?
>
> if this would be sufficient, you can change the default
> by putting: mol default color Element
> in your .vmdrc or vmd.rc file.

Coloring by element will certainly work for the OP as S and Si are
different elements.

My model is coarse-grained with non-element types like AA, AB, PA, PB,
PC, .... The molfile plugins call get_pte_idx which will return a 0
element number for any unknown string, but thanks for the tip anyways.
If it sufficiently bothers me in the future I can hack the molfile
plugin to assign phantom atomic numbers to unique particle types. For
now, I'm fine as I just renamed my particles so that 90% of the time I
want AA and AB colored the same anyways.

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