VMD-L Mailing List

From: Patzschke, Dr. Michael (patzsc21_at_hzdr.de)
Date: Fri Aug 31 2018 - 09:01:28 CDT

Hello,

I am using vmd to visualize metal complexes. It is customary and helpful, to
use a different style for the metal to ligand bonds as compared to the
intra-ligand bonds. Unfortunately, this seems not to be straight forward in
vmd.

I have had some success with defining a new rep. There I use something like
"all within 5 of name Eu" to define the area around the central ion (e.g.
europium), then I use Dynamic Bonds as the drawing method and change the
Distance Cutoff, so that all metal-ligand interactions are shown. I then use
a transparent material for these bonds.
The effect is quite pleasing, but the problem is, that this procedure also
leads to bonds between the ligand atoms. As the ligand-ligand atom distances
are very similar to the ligand-metal distances, there is no way to prevent
this from happening.

I also tried to add cylinders between the atoms of interest, but with
several eight-fold coordinated metal centres adding dozens of cylinders gets
very cumbersome. So I tried to cobble together a script:

proc glass_bond {} {
   global vmd_pick_atom vmd_pick_mol
   
   set sel1 [atomselect top "index 105"]
   set sel2 [atomselect $vmd_pick_mol "index $vmd_pick_atom"]
   
   # coordinates of metal
   set coords1 [lindex [$sel1 get {x y z}] 0]

   # coordinates of the atom
   set coords2 [lindex [$sel2 get {x y z}] 0]

   # and draw the line
   draw material BlownGlass
   draw cylinder $coords1 $coords2 radius 0.1

   puts "Start: $coords1"
   puts "End: $coords2"
}

This is a bit more practical, but one needs to change the first atomselect
by hand and start the script for every picked ligand atom.

Finally, I have tried the following approach, I measure the distance between
the atom pairs of interest and make the labels as small as possible, this
yields dotted lines between metal and ligand atoms. This is not extremely
beautiful and there is an additional problem. When I render this TachyonL
Optix, the dotted lines get blown up to enormous rings and are not usable.

Is there any simple way to produce the desired result in vmd I have
overlooked? Would anyone have a suggestions to improve my script so that one
can pick two atoms and then draw a cylinder between them. And even better
would it be possible to set the colour of the cylinders to that of the first
picked metal atom?

Kind regards,
Michael