this is all fixed now.
On Wed, Jul 1, 2009 at 3:20 AM, Robert Hanson <hans...@stolaf.edu> wrote:
> also, there's a bug in Jmol (now fixed, for next release) that "model=n"
> does not work. You have to say model=1.1 or */1 but not just model=1 . I
> checked back, and this bug dates to Jmol 11.6.RC17 -- LONG ago!
>
> Bob
>
> 2009/7/1 Angel Herráez <angel.herr...@uah.es>
>
> > 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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>>
>
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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