> On Tue, Jun 30, 2009 at 5:47 PM, Dan Connolly <conno...@w3.org>
> wrote:
> I'm struggling to understand how "define" works.
Hello Dan
"define" is rather simple, and dates back to Rasmol and Chime
scripting.
It's called a user-defined atom set. You give it a name and any atom
expression, and then you can use the name to specify that atom set.
For example:
define proteinNitrogens protein and nitrogen
define myBindingSite protein and *:A and within(3.0,ligand)
The name for the set may be anything as long as it is not a
JmolScript reserved word (that's why FGiJ is using the tilde for a
start), and it's case-insesitive as far as I reckon.
As for why the exact script you have is not working, it's likely a
bug as Bob says. Try another version of Jmol to check.
> select :c; define ~contarget (selected and model=1); select none;
> select ~contarget; spacefill
"select none" is trivial there: any selection overrides the previous
one.
Also, you can do that in several different variants:
define ~contarget (*:c and */1); select ~contarget; spacefill
define ~contarget (*:c and 1.0); select ~contarget; spacefill
Hope it helps
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