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