> Is there a scripting way to choose some bonds for different "fatness"
> than others.
Yes, you can set the size of each bond and each atom completely
Many script commands apply to the 'currently selected set of atoms'. So,
first we need a quick review of scripting the selection commands.
Hopefully all of these are obvious:
select all # OR select *
select carbon # OR elemno=6
select hydrogen or oxygen # OR select elemno=1,elemno=8
select not iron # OR select not iron
Here are some fancier ones:
select within(2.0, iron) # within 2.0 angstroms
select protein # only .pdb files
select ala,val # only .pdb files
select hetero and !water # only .pdb files
Once a selection is made, you can apply some rendering characteristics
to the currently selected set of atoms:
select carbon; color atoms blue; spacefill 25%
select hydrogen; spacefill off
But, you asked about bonds. It is a little more complicated because the
selection syntax only applies to atoms. By default, a bond is selected
only if both of its atoms are selected. So, if you want to make my
carbon-carbon bonds look attractive (or ugly) you can say:
select carbon; wireframe 0.2; color bonds magenta
The 'wireframe' and 'color bonds' commands only apply to bonds where
both atoms are in the selected set ... in this case carbons.
To give you some more control over the behavior of bond selections,
there is a setting called 'bondmode' which as values 'and' and 'or'. The
default value is 'and' ... meaning that the bond is selected only if
both atoms are selected ... both atom1 AND atom2. Changing the mode to
'or' means that the bond is selected if either atom is selected ...
either atom1 OR atom2.
So, let's say that I want to 'gussy up' all the bonds that include an
set bondmode or; select iron; wireframe 0.1; color bonds turquoise
> I am thinking of the Ferrocene example and a way to show
> the metal coordination bonding differently than the covalent bonding.
With ferrocene you should be able to do something like this:
#first work on oxygen
spacefill 0.25; #0.25 angstroms
color atoms lemonchiffon;
# bondmode defaults to AND ... restrict to only carbon-carbon bonds
color bonds mistyrose;
#now work on hydrogen
color atoms honeydew;
set bondmode or;
color bonds steelblue;
#finally the iron
color atoms firebrick;
#bondmode is still or
color bonds salmon;
You should, of course, choose your own colors :-)
* For more details on the RasMol scripting language that is used by Jmol
go to http://www.openrasmol.org/doc
* In general, script development works better in the Jmol application.
Later, move the script to the JmolApplet.
One more thing ... Jmol has a little-known feature that should work very
nicely for one of your ferrocene representations. If the file format is
.mol, then Jmol can render *aromatic* bonds.
1. get ferrocene.mol
2. go in and change the bond order to be '4' for the C-C bonds
3. reload, apply the script above, and enjoy!
(Actually, the aromaticFerrocene.mol is attached :-)