OK, I know what it is. You can't give
jmolApplet(...)
jmolLoadInline(..)
right in a row like that.
After jmolApplet the browser is busy creating the applet. VERY unwise to
fire commands at it while that is happening. In the past you could complete
crash the browser that way. I think what you want is to put that into a
script:
jmolApplet(...., script)
where script includes the
data "MODEL 1"
...
end "MODEL 1"
as shown at http://chemapps.stolaf.edu/jmol/docs/#data
That should work like a charm.
Bob
On Wed, Jan 13, 2010 at 7:10 PM, Grossman, Robert B <robert.gross...@uky.edu
> wrote:
> I'm still not having any luck seeing the molecule, even in 11.9.18.
>
> <script type="text/javascript">
> jmolInitialize('../../nosession/jmol');
> jmolApplet([250, 250]);
> jmolLoadInline('\n Marvin 12290623562D \n\n
> 23 26 0 0 0 0 999 V2000\n 4.3508 0.4841 0.0000 C 0
> 0 0 0 0 0 0 0 0 0 0 0\n 3.6363 0.0716 0.0000 C 0 0 0
> 0 0 0 0 0 0 0 0 0\n 3.6363 -0.7535 0.0000 C 0 0 0 0 0
> 0 0 0 0 0 0 0\n 4.3508 -1.1660 0.0000 C 0 0 0 0 0 0 0
> 0 0 0 0 0\n 5.0653 -0.7535 0.0000 C 0 0 0 0 0 0 0 0 0
> 0 0 0\n 5.0653 0.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
> 0\n 5.7797 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 5.7797 -1.1660 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 6.4942 -0.7535 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 6.4942 0.0716 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 6.4942 1.7216 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 5.7797 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 7.2087 0.4841 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 7.2087 1.3091 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 6.9067 -0.6429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 7.6212 -0.2304 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 8.4181 -0.4439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 3.9383 -1.8804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 4.7633 -1.8804 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 7.9231 1.7216 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n
> 5.0653 0.8966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> 5.0653 -1.5785 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n
> 5.7797 -0.3409 0.0000 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2
> 1 0 0 0 0\n 1 6 1 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0
> 0 0 0\n 4 5 1 0 0 0 0\n 4 18 1 0 0 0 0\n 4 19 1 0 0 0
> 0\n 6 5 1 0 0 0 0\n 5 8 1 0 0 0 0\n 5 22 1 0 0 0 0\n 7
> 6 1 0 0 0 0\n 6 21 1 0 0 0 0\n 7 10 1 0 0 0 0\n 12 7 1
> 0 0 0 0\n 7 23 1 0 0 0 0\n 8 9 1 0 0 0 0\n 9 10 1 0 0
> 0 0\n 10 13 1 0 0 0 0\n 10 15 1 0 0 0 0\n 11 12 1 0 0 0 0\n
> 11 14 1 0 0 0 0\n 13 14 1 0 0 0 0\n 13 16 1 0 0 0 0\n 14 20
> 2 0 0 0 0\n 16 15 2 0 0 0 0\n 16 17 1 0 0 0 0\nM END\n');
> </script>
>
> I think I must be missing something obvious here, but I can't figure out
> what.
>
> If it helps, Show -> Extract MOL data shows,
>
> zapped
> Jmol version 11.9.18 2010-01-12 17:49
> EXTRACT: visible
> 0 0 0 0 0
>
> -- Bob G.
>
> On 1/13/10 5:37 PM, "Robert Hanson" <hans...@stolaf.edu> wrote:
>
> Works fine in Jmol 11.9.18. Unfortunately we JUST released 11.8.16, and I
> missed this fix in there. Please at least try the Jmol 11.9.
>
> On Wed, Jan 13, 2010 at 3:41 PM, Grossman, Robert B <
> robert.gross...@uky.edu> wrote:
> Hi, I spoke too soon before. I have a new problem. Now Jmol is only
> occasionally displaying the molecule. For example, this script gives a
> blank Jmol:
>
> <script type="text/javascript">
> // <!--
> function getMol_0() {
> return '\n Marvin 10270415522D\n\n 9 9 0 0 0 0
> 999 V2000\n -2.2457 0.8188 0.0000 C 0 0 0 0 0 0 0 0 0 0
> 0 0\n -2.2457 -0.0063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
> 0\n -1.5313 -0.4188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -0.8168 -0.0063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -0.8168 0.8188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -0.1023 1.2313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 1.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 2.8813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 2.0563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7 1
> 1 0 0 0 0\n 7 5 2 0 0 0 0\n 1 2 2 0 0 0 0\n 2 3 1 0
> 0 0 0\n 3 4 2 0 0 0 0\n 4 5 1 0 0 0 0\n 5 6 1 0 0 0
> 0\n 8 9 1 0 0 0 0\n 7 9 1 0 0 0 0\nM APO 1 9 1\nM STY
> 1 1 SUP\nM SAL 1 2 8 9\nM SBL 1 1 9\nM SMT 1 Et\nM
> END\n';
> }
> // -->
> </script>
>
>
> <script type="text/javascript">
> jmolInitialize('../nosession/jmol');
> jmolApplet([250, 250]);
> jmolLoadInline(getMol_0());
> </script>
>
>
> As does this:
>
> <p style="text-align:center;">
> <script type="text/javascript">
> jmolInitialize('../../nosession/jmol');
> jmolApplet([250, 250]);
> jmolLoadInline('\n Marvin 10270415522D\n\n 9 9 0 0
> 0 0 999 V2000\n -2.2457 0.8188 0.0000 C 0 0 0 0 0
> 0 0 0 0 0 0 0\n -2.2457 -0.0063 0.0000 C 0 0 0 0 0 0 0
> 0 0 0 0 0\n -1.5313 -0.4188 0.0000 C 0 0 0 0 0 0 0 0 0
> 0 0 0\n -0.8168 -0.0063 0.0000 C 0 0 0 0 0 0 0 0 0 0 0
> 0\n -0.8168 0.8188 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -0.1023 1.2313 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 1.2313 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 2.8813 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n
> -1.5313 2.0563 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 7 1
> 1 0 0 0 0\n 7 5 2 0 0 0 0\n 1 2 2 0 0 0 0\n 2 3 1 0
> 0 0 0\n 3 4 2 0 0 0 0\n 4 5 1 0 0 0 0\n 5 6 1 0 0 0
> 0\n 8 9 1 0 0 0 0\n 7 9 1 0 0 0 0\nM APO 1 9 1\nM STY
> 1 1 SUP\nM SAL 1 2 8 9\nM SBL 1 1 9\nM SMT 1 Et\nM
> END\n');
> </script>
> </p>
>
> Once in a while I can induce Jmol to give me a picture, but it's not
> reproducible.
>
> Any ideas?
>
> Now using Jmol 11.8.10.
>
> ________________________________
> From: Angel Herráez <angel.herr...@uah.es>
> Reply-To: <jmol-users@lists.sourceforge.net>
> Date: Wed, 13 Jan 2010 15:28:46 -0500
> To: <jmol-users@lists.sourceforge.net>
> Conversation: [Jmol-users] Jmol demo page hangs
> Subject: Re: [Jmol-users] Jmol demo page hangs
>
> Yes, I see the same: the applet ends loading, but stays empty.
> Try changing to JmolApplet 11.8.10
> It works for me with your code
>
>
>
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> attendees to learn about information security's most important issues
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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
------------------------------------------------------------------------------
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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