OK, after some fiddling around with 11.9.18, I believe I have it working.
"javascript: appletLoaded();" is incorrect; it needs to be "javascript
appletLoaded();" (no colon).
jmolAppletInline() hangs.
However, this works:
function jmolLoaded() {
jmolLoadInline('\n Marvin 03180516593D\n\n 22 22 0
0 0 0 999 V2000\n -0.4201 0.2577 -1.4146 C 0 0 0 0 0
0 0 0 0 6 0 0\n 1.0119 0.6024 -0.9257 C 0 0 2 0 0 0 0 0
0 5 0 0\n 1.4430 -0.3157 0.2489 C 0 0 2 0 0 0 0 0 0 4 0
0\n 0.4201 -0.2577 1.4146 C 0 0 0 0 0 0 0 0 0 3 0 0\n
-1.0119 -0.6024 0.9257 C 0 0 0 0 0 0 0 0 0 2 0 0\n -1.4430
0.3157 -0.2489 C 0 0 0 0 0 0 0 0 0 1 0 0\n -0.7193 0.9460
-2.2082 H 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4212 -0.7482
-1.8450 H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.7207 0.5093 -1.7516
H 0 0 0 0 0 0 0 0 0 0 0 0\n 1.5221 -1.3462 -0.1098 H 0 0
0 0 0 0 0 0 0 0 0 0\n 0.7193 -0.9460 2.2082 H 0 0 0 0 0
0 0 0 0 0 0 0\n 0.4212 0.7482 1.8450 H 0 0 0 0 0 0 0 0
0 0 0 0\n -1.7207 -0.5093 1.7516 H 0 0 0 0 0 0 0 0 0 0 0
0\n -1.0386 -1.6454 0.5961 H 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.5221 1.3462 0.1098 H 0 0 0 0 0 0 0 0 0 0 0 0\n -2.4331
0.0241 -0.6065 H 0 0 0 0 0 0 0 0 0 0 0 0\n 2.8389 0.0954
0.7531 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.0495 2.0704
-0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.3832 2.8404 -0.4618
C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.2742 2.8574 -0.4618 C 0 0
0 0 0 0 0 0 0 0 0 0\n 4.1725 -0.6746 0.7531 C 0 0 0 0 0
0 0 0 0 0 0 0\n 5.4409 -0.0177 1.3286 C 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 5 6 1 0 0 0 0\n 1 7
1 0 0 0 0\n 1 8 1 0 0 0 0\n 2 9 1 0 0 0 0\n 2 18 1 0 0 0
0\n 3 17 1 0 0 0 0\n 3 10 1 0 0 0 0\n 4 11 1 0 0 0 0\n 4 12
1 0 0 0 0\n 5 13 1 0 0 0 0\n 5 14 1 0 0 0 0\n 6 15 1 0 0
0 0\n 6 16 1 0 0 0 0\n 17 21 1 0 0 0 0\n 18 19 1 0 0 0 0\n 18
20 1 0 0 0 0\n 21 22 1 0 0 0 0\nM END\n');
}
jmolInitialize('../../nosession/jmol');
var jmolScript = 'javascript jmolLoaded(); ';
jmolApplet([250, 250], jmolScript);
________________________________
From: Robert Hanson <hans...@stolaf.edu>
Reply-To: <jmol-users@lists.sourceforge.net>
Date: Thu, 14 Jan 2010 12:29:31 -0500
To: <jmol-users@lists.sourceforge.net>
Conversation: [Jmol-users] Jmol usually not displaying molecule
Subject: Re: [Jmol-users] Jmol usually not displaying molecule
The key is that the jmolApplet command - or whatever is used to create the
applet - must be the last command given until the applet itself reports that it
is present and accounted for, and page loading is complete. This is very
important.
If you have a lot of stuff that doesn't work as a Jmol script, then what you do
is put this code at the end of the script sent to Jmol with applet creation:
javascript: appletLoaded();
this would then run a JavaScript function "appletLoaded()" on the page to
notify the page that the applet is loaded, its initial script is complete, and
it is ready for commands.
Bob
On Thu, Jan 14, 2010 at 10:37 AM, Grossman, Robert B <robert.gross...@uky.edu>
wrote:
Hm, seems to me there needs to be some documentation on this problem.
So, are there never supposed to be any commands following the jmolApplet()
command? If not, could the jmolLoadInline() command, or any other command,
precede the jmolApplet() command? That is, could I have a long list of
commands as long as the jmolApplet() command was last?
I will try the jmolAppletInline() solution.
________________________________
From: Robert Hanson <hans...@stolaf.edu>
Reply-To: <jmol-users@lists.sourceforge.net>
Date: Wed, 13 Jan 2010 23:05:55 -0500
To: <jmol-users@lists.sourceforge.net>
Conversation: [Jmol-users] Jmol usually not displaying molecule
Subject: Re: [Jmol-users] Jmol usually not displaying molecule
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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--
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
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
--
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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