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
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
> ------------------------------------------------------------------------------
> This SF.Net email is sponsored by the Verizon Developer Community
> Take advantage of Verizon's best-in-class app development support
> A streamlined, 14 day to market process makes app distribution fast and
> easy
> Join now and get one step closer to millions of Verizon customers
> http://p.sf.net/sfu/verizon-dev2dev
> _______________________________________________
> Jmol-users mailing list
> Jmol-users@lists.sourceforge.net
> https://lists.sourceforge.net/lists/listinfo/jmol-users
>
>
>
>
>
> ------------------------------------------------------------------------------
> 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
> _______________________________________________
> 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
_______________________________________________
Jmol-users mailing list
Jmol-users@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/jmol-users
