Drawing a box around a molecule

 

Here's a quick function to draw a box around a molecule. Delete any graphics you may have loaded and enter this script.

proc box_molecule {molid} {
      # get the min and max values for each of the directions
      # (I'm not sure if this is the best way ... )
      set sel [atomselect top all]

      set coords [lsort -real [$sel get x]]
      set minx [lindex $coords 0]
      set maxx [lindex [lsort -real -decreasing $coords] 0]

      set coords [lsort -real [$sel get y]]
      set miny [lindex $coords 0]
      set maxy [lindex [lsort -real -decreasing $coords] 0]

      set coords [lsort -real [$sel get z]]
      set minz [lindex $coords 0]
      set maxz [lindex [lsort -real -decreasing $coords] 0]

      # and draw the lines
      draw materials off
      draw color yellow
      draw line "$minx $miny $minz" "$maxx $miny $minz"
      draw line "$minx $miny $minz" "$minx $maxy $minz"
      draw line "$minx $miny $minz" "$minx $miny $maxz"

      draw line "$maxx $miny $minz" "$maxx $maxy $minz"
      draw line "$maxx $miny $minz" "$maxx $miny $maxz"

      draw line "$minx $maxy $minz" "$maxx $maxy $minz"
      draw line "$minx $maxy $minz" "$minx $maxy $maxz"

      draw line "$minx $miny $maxz" "$maxx $miny $maxz"
      draw line "$minx $miny $maxz" "$minx $maxy $maxz"

      draw line "$maxx $maxy $maxz" "$maxx $maxy $minz"
      draw line "$maxx $maxy $maxz" "$minx $maxy $maxz"
      draw line "$maxx $maxy $maxz" "$maxx $miny $maxz"
}

If you don't already have a molecule loaded, load one, e.g.,
mol load pdb $env(VMDDIR)/proteins/alanin.pdb
and make it the top molecule. Then execute the command:

  box_molecule top

(you could also enter the molecule id instead of top).