Here is what happened on my MacBook Pro running OS X 10.6.2 with Java 1.6.0_17.
After entering the ~alert(bobFile); then clicking on Run I got the following:
Marvin 12290623562D
23 26 0 0 0 0 999 V2000
4.3508 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6363 0.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.6363 -0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.3508 -1.1660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0653 -0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0653 0.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7797 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7797 -1.1660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4942 -0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4942 0.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4942 1.7216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.7797 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2087 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2087 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.9067 -0.6429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.6212 -0.2304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.4181 -0.4439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.9383 -1.8804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.7633 -1.8804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.9231 1.7216 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
5.0653 0.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
5.0653 -1.5785 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
5.7797 -0.3409 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
1 6 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
4 18 1 0 0 0 0
4 19 1 0 0 0 0
6 5 1 0 0 0 0
I'm pretty sure this was not the end of the file. The window that popped up
containing this seemed to extend off the bottom of the screen and I couldn't
scroll down. Hitting return closed the window (normal for an alert).
Next I entered the second command,
~document.getElementById(pickApplet).loadInlineString(bobFile, "", false); This
loaded a new molecule. The molecule was strange in that it was completely flat
with several atoms overlapping. I don't know if that is how the structure
should be, but it looked very odd.
Hope this helps.
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***********************************************
On Jan 13, 2010, at 9:46 PM, Otis Rothenberger wrote:
> Hi Again Bob,
>
> I don't know if this will help, but I put your latest coordinate file
> string into a JavaScript variable called bobFile on the following
> page:
>
> http://chemagic.com/web_molecules/script_page_large.aspx
>
> bobFile was not altered. It has the \n's.
>
> The page uses Jmol 11.9.9.
>
> There is a JavaScript Jmol Script execution field on the page.
> JavaScript commands require a leading tilde. Further, the tilde must
> be the first character in the field with no space between the tilde
> and the JavaScript command. Click Run to see script results. On my
> Windows XP platform, the following commands are instructive:
>
> ~alert(bobFile);
>
> ~document.getElementById(pickApplet).loadInlineString(bobFile, "", false);
>
> pickApplet is my variable for the applet name. The above command,
> including the tilde, is good to go. Remember, the tilde makes my page
> interpret this as JavaScript.
>
> On my machine, the alert, of course, shows the string, sans the \n -
> i.e. Jmol is reading them as intended. The direct call of the applet
> method properly loads the string.
>
> I should mention that I do not use jmol.js. I use a cross browser object tag.
>
> I do not have quick access to a Mac, so I'm interested in how a Mac
> responds to this page. I hope the above information is of some use to
> you. As an aside, check out Jmol's UFF fuction on your model once
> (if?) it loads (UFF link). I think this relatively new addition to
> Jmol is really neat.
>
> Otis
>
> --
> Otis Rothenberger
> http://chemagic.org
>
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Throughout its 18-year history, RSA Conference consistently attracts the
world's best and brightest in the field, creating opportunities for Conference
attendees to learn about information security's most important issues through
interactions with peers, luminaries and emerging and established companies.
http://p.sf.net/sfu/rsaconf-dev2dev
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