From: Josh Vermaas (
Date: Fri Aug 08 2014 - 15:23:20 CDT

Hi Fikret,

Cutting it in half is the easy part.
Extensions->Visualizations->Clipping Plane Tool is what you want.

The harder part is dealing with the different atomtypes. According to
the docs (,
what *should* work (assuming you have an atomtype CZ that you want to
color blue), and doesn't give any error when you run it, is the
following TkConsole command:

color add item Type CZ blue

The only problem with this approach is that the default atomtypes (In
this case C) seem to preempt the new atomtype, and any CZ type atoms
don't change color like we want them to. I don't have the time to track
down, but in the interim what you do is make the atomtype something else
and be happy:

set sel [atomselect top "type CZ"]
color add item Type Q blue
$sel set type Q

Note that the color add item commands are case sensitive (Type is what
things get colored by, not type).

-Josh Vermaas
On 8/8/14, 1:58 PM, Fikret Aydin wrote:
> Hello Everyone,
> I have 10 atom types in my system and I can give them different colors
> by using the "Name" category in the VMD color controls but it only
> shows up to 9 different types. I can't see "Type 10" in the list so I
> am not able to change the color of that type. Is there any way to
> change the color of that type?
> Also, I am wondering if there is any way to visualize only half of a
> structure (by cutting it from the center of mass)?
> Thanks a lot in advance,
> Fikret