Not a problem -- communication is rarely perfect, Otis.
OK, that should be fixed. The problem was in the way that the addition of
hydrogen atoms worked. It was adding hydrogens by appending a script --
well, if you do that, then it runs, but at the wrong time! All of the first
script runs, then the hydrogens are added! Tricky bug.
Let's give this a try now.
http://chemapps.stolaf.edu/jmol.docs/examples-11/Jmol-11.zip
On Mon, Feb 15, 2010 at 7:21 PM, Otis Rothenberger <[email protected]>wrote:
> Bob-
>
> I apologize for the incomplete information. The timing problems that I'm
> having may actually be Jmol bugs, so I'll document an important case below.
>
> 1) I load ethane.
> 2) I run following Jmol script:
>
> {atomIndex=3}.element = "C";minimize addHydrogens;select hydrogen and
> connected({atomIndex=3});delete selected
>
>
excellent test script -- this did the trick.
> The script only executes "{atomIndex=3}.element = "C";minimize
> addHydrogens;"
>
> If, however, I run the script in two separate steps (I'm using an execute
> script text field on my page.), the two sequential steps do what I expected:
>
>
right, because Jmol was adding the hydrogens AFTER, not before, minimizing.
> Step 1: select hydrogen and connected({atomIndex=3});delete selected;
> Step 2: {atomIndex=3}.element = "C";minimize addHydrogens;
>
> As expected, these two steps run separately add a carbon, add hydrogens,
> and then delete these hydrogens. I've been calling my encounter with this
> type of problem a "timing problem," but timing may not be the problem.
>
>
Well, it was timing, but not YOUR problem -- mine!
Bob
--
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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