VMD-L Mailing List

From: Joshua Anderson (joaander_at_umich.edu)
Date: Fri Apr 16 2010 - 11:09:23 CDT

I myself ran into this issue a few weeks ago. I dug around in the VMD
source code and found that while it retains the full type name for
features such as atom selections, the name is always truncated to the
first alpha character and then uppercased for coloring by type and
name. This "feature" is buried deep in the C++ code of VMD and there
didn't appear to be an option

I setup a script to create many representations (one for each type)
and color by color ID to work around this problem.
--------
Joshua A. Anderson, Ph.D.
Chemical Engineering Department, University of Michigan

On Apr 16, 2010, at 9:15 AM, Jennifer Williams wrote:

>
>
> Hi,
>
> I have a structure and need to change the colours of certain atoms.
> In my .pdb file I have SI and S. Both are automatically recognized
> as S in VMD and given the same colour. I am unable to change this
> using the colour control in the graphical interface.
>
> I know that I could easily do find and replace in my .pdb file but I
> also have trajectory files which I cannot format.
>
> Is there someone around this -perhaps using some script command. Any
> help greatly appreciated,
>
> Jenny
>
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
>
>