CCL: show ruler in VMD

[John Stone <johns()ks.uiuc.edu>]

Hi,
   My coworker Jordi wrote up a useful VMD script for displaying a
 "ruler" grid that automatically rescales along with the molecule.
 This script could be modified slightly to draw various other scale bars
 if you prefer something different, but it should be a good starting
 point as it handles the trickiest parts such as automatically updating
 when the user zooms in and out etc.  I've attached the script to this email.
 Cheers,
   John Stone
   vmd[A]ks.uiuc.edu
 On Wed, May 30, 2007 at 09:33:09AM +0300, Liisa laakkonen
 llaakkon::cc.helsinki.fi wrote:
 >
 > Sent to CCL by: Liisa laakkonen [llaakkon===cc.helsinki.fi]
 > Hello Yubo,
 >
 > 	I've done the angstrom ruler simply by building a dummy pdb with
 > enough points to measure the desired distance, and displaying it side
 > by side with my molecule. Works equally well for a compass.
 >
 > 	Greetings,
 > 	Liisa
 >
 > liisa.laakkonen ~ helsinki.fi
 >
 > On Tue, May 29, 2007 at 09:29:44AM -0400, Chelsey Crosse cmcrosse*_*mtu.edu
 wrote:
 > > Yubo,
 > >
 > > The only way that I know of to put a ruler in VMD by opening the Tcl
 > > console and drawing it in yourself.  However, I'm not positive about
 > > how accurate you can make it.
 > >
 > > Chelsey
 > >
 > > On 25 May 2007, at 10:17, Yubo Fan yubofan(0)mail.chem.tamu.edu wrote:
 > >
 > > > Hello,
 > > >
 > > > A quick question about VMD. Is there any way to show ruler (ie
 > > > angstroms in unit) in VMD window?
 > > >
 > > > Thanks,
 > > >
 > > > Yubo
 > > > ============================================================
 > > > Dr. Yubo Fan               Email: yubofan^^^mail.chem.tamu.edu
 > > > Department of Chemistry    Tel:   1-979-845-5237
 > > > Texas A&M University
 > > > College Station, TX 77843
 > > > ============================================================
 > > >
 > >
 >
 >
 --
 NIH Resource for Macromolecular Modeling and Bioinformatics
 Beckman Institute for Advanced Science and Technology
 University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
 Email: johns[A]ks.uiuc.edu                 Phone: 217-244-3349
   WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078

# Overlays
 # Author: Jordi Cohen
 #
 # For now, implements a grid overlay
 namespace eval ::Overlays:: {
   set grid_on 0
   set grid_dirty 1  ;# ruler needs a refresh
   set grid_scale 0
   set grid_scale_graphics_id -1
   set grid_mol -1
 }
 proc ::Overlays::setup_grid {} {
   variable grid_mol
   variable grid_on
   variable grid_dirty
   set top [molinfo top]
   set grid_mol [mol new]
   mol rename $grid_mol "Grid"
   if {$top >= 0} {
     mol top $top
     molinfo $grid_mol set scale_matrix [molinfo $top get scale_matrix]
   }
   redraw_grid
   trace add variable ::vmd_logfile write ::Overlays::logfile_cb
   set grid_on 1
   set grid_dirty 1
 }
 proc ::Overlays::remove_grid {} {
   variable grid_mol
   variable grid_on
   trace remove variable ::vmd_logfile write ::Overlays::logfile_cb
   mol delete $grid_mol
   set grid_on 0
 }
 proc ::Overlays::redraw_grid {} {
   variable grid_mol
   variable grid_on
   variable grid_scale
   variable grid_dirty
   variable grid_scale_graphics_id
   molinfo $grid_mol set center_matrix [list [transidentity]]
   molinfo $grid_mol set rotate_matrix [list [transidentity]]
   molinfo $grid_mol set global_matrix [list [transidentity]]
   set realscale [lindex [molinfo $grid_mol get scale_matrix] 0 0 0]
   set scale [expr round(-log10($realscale))-1]
   if {$scale != $grid_scale} {set grid_dirty 1}
   set display_ratio [expr 1.*[lindex [display get size] 0]/[lindex [display get
 size] 1]]
   set div [expr pow(10,$scale)]
   if {$grid_dirty} {
     set grid_scale $scale
     set minx [expr -200*$div]
     set maxx [expr 200*$div]
     set miny [expr -50*$div]
     set maxy [expr 50*$div]
     graphics $grid_mol delete all
     graphics $grid_mol  color gray
   #  draw material Transparent
     for {set tick $minx} {$tick <= $maxx} {set tick [expr $tick + $div]} {
       graphics $grid_mol  line [list $tick $miny 0] [list $tick $maxy 0] width 1
 style dashed
     }
     for {set tick $miny} {$tick <= $maxy} {set tick [expr $tick + $div]} {
       graphics $grid_mol  line [list $minx $tick 0] [list $maxx $tick 0] width 1
 style dashed
     }
     draw color gray
 #  draw material Opaque
     for {set tick $minx} {$tick <= $maxx} {set tick [expr $tick + 10.*$div]}
 {
       graphics $grid_mol line [list [expr $tick] $miny 0] [list [expr $tick]
 $maxy 0] width 2
     }
     for {set tick $miny} {$tick <= $maxy} {set tick [expr $tick + 10.*$div]}
 {
       graphics $grid_mol  line [list $minx $tick 0] [list $maxx $tick 0] width 2
     }
     set grid_scale_graphics_id [graphics $grid_mol text [list [expr
 1.2*$display_ratio/$realscale] [expr -1.4/$realscale] 0] "[format
 "%g" $div]A" size 0.8]
     set grid_dirty 0
   } else {
     graphics $grid_mol delete $grid_scale_graphics_id
     set grid_scale_graphics_id [graphics $grid_mol text [list [expr
 1.2*$display_ratio/$realscale] [expr -1.4/$realscale] 0] "[format
 "%g" $div]A" size 0.8]
   }
 }
 proc ::Overlays::logfile_cb { args } {
   variable grid_mol
   # Check for display transforms
   if { [string match "rotate*" $::vmd_logfile] || [string match
 "translate*" $::vmd_logfile] || \
             [string match "scale*" $::vmd_logfile] || [string match
 "display*" $::vmd_logfile]} {
     redraw_grid
   }
 }
 proc ::Overlays::overlay {args} {
   variable grid_mol
   variable grid_on
   set overlay [lindex $args 0]
   set state [string is true [lindex $args 1]]
   if {"$overlay" == "grid"} {
     if {$state} {
       if {$grid_on} {remove_grid}
       setup_grid
     } else {
       if {$grid_on} {remove_grid}
     }
   } else {
     puts "overlay: Unknown overlay"
   }
 }
 proc overlay {args} {
   eval ::Overlays::overlay $args
 }
 overlay grid on