VMD-L Mailing List

From: Justin Gullingsrud (justin_at_ks.uiuc.edu)
Date: Wed Jun 18 2003 - 09:22:42 CDT

On Wed, Jun 18, 2003 at 02:02:39PM +0800, #WONG CHEE HOW# wrote:
> Hi,
>
> I am using VMD1.8 and wondering is it possible that the program will allow me to colour the space enclosed by, say, 6 atoms bonded together? In addition, if I have 1200 atoms all randomly inside a cube of 10 angstrom x 10 angstrom x 10 angstrom, is it possible to make VMD only display the atoms at the top half, bottom half, left hand side, or right hand side of the cube as I desired?
>

Hi,

You could draw a triangle for each set of three atoms in the set, with vertices
at those atoms; that way you would be guaranteed to enclose the space. A
script for that would look something like:

set sel [atomselect top "my six atoms"]
set atompos [$sel get {x y z}]
set n [$sel num]
for { set i 0 } { $i < $n } { incr i } {
  set pi [lindex $atompos $i]
  for { set j [expr $i + 1] } { $j < $n } { incr j } {
    set pj [lindex $atompos $j]
    for { set k [expr $j + 1] } { $k < $n } { incr k } {
      set pk [lindex $atompos $k]
      draw triangle $pi $pj $pk
    }
  }
}

BTW, you can delete all the triangles with "draw delete all". To draw in
a different color, enter "draw color red" or whatever before you start
drawing (i.e. just before the first for loop).

For the atoms in the cube, that's easy: just select "x < 0", "y > 0", etc.
assuming the box is centered at the origin. If not you'll have to adjust
the position of the cutoff accordingly.

Cheers,
Justin

      

> Thanks in advance.
>
> Regards,
> CH WONG 

-- 
  Justin Gullingsrud        3111 Beckman Institute        217-244-8946
  I been dropping the new science, and I be kicking the new knowledge,
  and I'm seeing to a degree that you can't get in college.  -- b.boys