VMD-L Mailing List

From: Justin Gullingsrud (jgulling_at_mccammon.ucsd.edu)
Date: Thu Mar 11 2004 - 08:23:31 CST

On Thu, Mar 11, 2004 at 06:11:40PM +0900, DongHoon Chung wrote:
> Hello..
>
> I would like to color atoms based on the distance from the specific point,
> not from the center of the molecule as POS method. And also I would like to
> make color scale or change in that method or POS method too, like GRASP
> z-depth cueing. Any suggestion will be helpful.

I'm not sure I understand your second question. If you want to color by
the z coordinate, what you could do type the following at the command
line:

  set all [atomselect top all]
  $all set beta [$all get z]

Then switch the coloring method to Beta. You can change the color scale
parameters in the Color menu. Note that moving the molecule around won't
automatically update the colors like it did when you colored by position;
you'd have to type "$all set beta [$all get z]" again to see the effect.

Cheers,
Justin

>
> Regards..
>
>
>
>
>
>
>
> DongHoon Chung Ph.D
>
>
>
> Department of microbiology
>
> College of Med. Korea University.
>
> -------------------------------------------
>
> It is a question that drives us................in The Matrix
>
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>