Re: [Jmol-users] Jmol usually not displaying molecule
Robert Hanson wrote: 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. Yes, I've often had similar problems with jmolApplet(...) jmolScript(..) The solution was to put the initial script inside the jmolApplet() call. How about using jmolAppletInline() ? That's what it is designed for, right? Previously, Jeff Hansen wrote: 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). I've seen that too. It's just a very long alert. The browser (Firefox in WinXP) does not put scrollbars on alert boxes. 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. It is. The data in that example say Z=0 for all atoms. And previously, Grossman, Robert B wrote: 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 That's OK, Bob G. If the model hasn't loaded, Jmol will give you nothing. -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
2010/1/14 Angel Herráez angel.herr...@uah.es How about using jmolAppletInline() ? That's what it is designed for, right? yes! Of course. I forgot that! Definitely that is the way to go here. -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
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 0999 V2000\n4.35080.48410. C 0 0 0
0 0 0 0 0 0 0 0 0\n3.63630.07160. C 0 0 0 0 0 0
0 0 0 0 0 0\n3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0
0 0 0\n4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0
0\n5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0\n5.7797
0.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n5.7797 -1.1660
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n6.4942 -0.75350.
C 0 0 0 0 0 0 0 0 0 0 0 0\n6.49420.07160. C 0 0
0 0 0 0 0 0 0 0 0 0\n6.49421.72160. C 0 0 0 0 0
0 0 0 0 0 0 0\n5.77971.30910. C 0 0 0 0 0 0 0 0
0 0 0 0\n7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0
0\n7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0\n7.6212
-0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0\n8.4181 -0.4439
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n3.9383 -1.88040.
C 0 0 0 0 0 0 0 0 0 0 0 0\n4.7633 -1.88040. C 0 0
0 0 0 0 0 0 0 0 0 0\n7.92311.72160. O 0 0 0 0 0
0 0 0 0 0 0 0\n5.06530.89660. C 0 0 0 0 0 0 0 0
0 0 0 0\n5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0
0\n5.7797 -0.34090. 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 0999
V2000\n -2.24570.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5313
-0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8168
-0.00630. C 0
Re: [Jmol-users] Jmol usually not displaying molecule
With Jmol 11.9.18, Safari 4.0.4, MacOS 10.5.8, and the following code:
script type=text/javascript
jmolInitialize('../../nosession/jmol');
jmolAppletInline([250, 250], '\n Marvin 10270415522D\n\n
9 9 0 0 0 0999 V2000\n -2.24570.81880. C 0 0
0 0 0 0 0 0 0 0 0 0\n -2.2457 -0.00630. C 0 0 0 0 0
0 0 0 0 0 0 0\n -1.5313 -0.41880. C 0 0 0 0 0 0 0 0
0 0 0 0\n -0.8168 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0
0\n -0.81680.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.10231.23130. O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5313
1.23130. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53132.8813
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53132.0563
0. 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
Jmol tells me that it is loading the applet, the clock begins, and the
structure never loads.
Same is true of this code:
script type=text/javascript
// !--
function getMol_0() {
return '\n Marvin 10270415522D\n\n 9 9 0 0 0 0999
V2000\n -2.24570.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5313
-0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8168
-0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.81680.8188
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.10231.23130.
O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53131.23130. C 0 0
0 0 0 0 0 0 0 0 0 0\n -1.53132.88130. C 0 0 0 0 0
0 0 0 0 0 0 0\n -1.53132.05630. 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
table style=margin-left:auto; margin-right:auto;
trtd style=text-align:center;
script type=text/javascript
jmolInitialize('../nosession/jmol');
jmolAppletInline([250, 250], getMol_0(),
'background [xf6edf7];');
/script
/td
/tr
/table
Sorry to be so much trouble.
-- Bob G.
From: Robert Hanson hans...@stolaf.edu
Reply-To: jmol-users@lists.sourceforge.net
Date: Thu, 14 Jan 2010 11:19:40 -0500
To: jmol-users@lists.sourceforge.net
Conversation: [Jmol-users] Jmol usually not displaying molecule
Subject: Re: [Jmol-users] Jmol usually not displaying molecule
2010/1/14 Angel Herráez angel.herr...@uah.es
How about using jmolAppletInline() ?
That's what it is designed for, right?
yes! Of course. I forgot that! Definitely that is the way to go here.
--
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
Re: [Jmol-users] Jmol usually not displaying molecule
Hello Again B, B, and A, Just a thought because I went to bed thinking about this last night: Does jmolAppletInline([250, 250], '\n Marvin ETC pickup Bob's apostrophe quotes? If so, then I think the regular expression in _jmolSterilizeInline(model) is simply changing them back to apostrophe quotes (#39;). Is that the intent? I'm using Jmol 11.9.9. Otis -- Otis Rothenberger http://chemagic.org -- 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
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 0999 V2000\n4.35080.48410. C 0
0 0 0 0 0 0 0 0 0 0 0\n3.63630.07160. C 0 0 0
0 0 0 0 0 0 0 0 0\n3.6363 -0.75350. C 0 0 0 0 0
0 0 0 0 0 0 0\n4.3508 -1.16600. C 0 0 0 0 0 0 0
0 0 0 0 0\n5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0
0 0 0\n5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0
0\n5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0\n
3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0\n
5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0\n
5.7797 -0.34090. 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
Re: [Jmol-users] Jmol usually not displaying molecule
Javascript accepts strings inside both single and double quotes, so it shouldn't. A student programmer whose name is lost in the mists of time made the decision to put our program's Javascript variables in single quotes, and we have been stuck with it ever since. (Stuck with it because it would be too much trouble to go through the entire app and change '' to , and it needs always to be one or the other so that we know how to modify Java strings so that they don't cause parsing errors when we place their values in a Javascript string.) From: Otis Rothenberger o...@chemagic.com Reply-To: jmol-users@lists.sourceforge.net Date: Thu, 14 Jan 2010 12:28:22 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Jmol usually not displaying molecule Subject: Re: [Jmol-users] Jmol usually not displaying molecule Hello Again B, B, and A, Just a thought because I went to bed thinking about this last night: Does jmolAppletInline([250, 250], '\n Marvin ETC pickup Bob's apostrophe quotes? If so, then I think the regular expression in _jmolSterilizeInline(model) is simply changing them back to apostrophe quotes (#39;). Is that the intent? I'm using Jmol 11.9.9. Otis -- Otis Rothenberger http://chemagic.org -- 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 -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
El 14 Jan 2010 a las 11:45, Grossman, Robert B escribió: With Jmol 11.9.18, Safari 4.0.4, MacOS 10.5.8, and the following code: I'm not sure, but probably 11.9.18 has the same bug as 11.8.15, 11.8.16 and 11.9.13. The fix has been done recently and is not yet available for download. You can either switch to 10.8.10 or a to a fomre 11.9.x (not sure which one), or get the latest 11.9 from Bob's site, http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip El 14 Jan 2010 a las 11:37, Grossman, Robert B escribió: Hm, seems to me there needs to be some documentation on this problem. Good idea, I'll add something in http://jmol.sourceforge.net/jslibrary/#jmolApplet http://jmol.sourceforge.net/jslibrary/#jmolAppletInline but it will take some time to show up until the next update of the website -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
The version I have most recently downloaded, 11.9.18, is the one from Bob's site. From: Angel Herráez angel.herr...@uah.es Reply-To: jmol-users@lists.sourceforge.net Date: Thu, 14 Jan 2010 12:47:47 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Jmol usually not displaying molecule Subject: Re: [Jmol-users] Jmol usually not displaying molecule El 14 Jan 2010 a las 11:45, Grossman, Robert B escribió: With Jmol 11.9.18, Safari 4.0.4, MacOS 10.5.8, and the following code: I'm not sure, but probably 11.9.18 has the same bug as 11.8.15, 11.8.16 and 11.9.13. The fix has been done recently and is not yet available for download. You can either switch to 10.8.10 or a to a fomre 11.9.x (not sure which one), or get the latest 11.9 from Bob's site, http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip El 14 Jan 2010 a las 11:37, Grossman, Robert B escribió: Hm, seems to me there needs to be some documentation on this problem. Good idea, I'll add something in http://jmol.sourceforge.net/jslibrary/#jmolApplet http://jmol.sourceforge.net/jslibrary/#jmolAppletInline but it will take some time to show up until the next update of the website -- 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 -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
El 14 Jan 2010 a las 12:48, Grossman, Robert B escribió: The version I have most recently downloaded, 11.9.18, is the one from Bob's site. Current is 11.9.19_dev, dated 14 Jan. Try that, so we can clarify the issue -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
Sorry for the possible confusion, I see that the date of the latest file in Bob's site is 14 Jan, but the popup menu reports 12 Jan. A better idea: I remembered about one of Bob's tricks: you can view any Jmol webpage using any version of the applet. This is documented at http://wiki.jmol.org/index.php?title=Backward_compatibility#Testing_di fferent_applet_versions So I tried the page that started all this discussion using Bob's latest applet: http://jmol.sourceforge.net/demo/jssample2/?JMOLJAR=http://chemapps.st olaf.edu/jmol/docs/examples-11/JmolApplet0.jar It works. Now try yours -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
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 -2.24570.81880. C 0 0 0 0 0 0 0 0 0 0
0 0\n -2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0
0\n -1.5313 -0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.8168 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.81680.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.10231.23130. O 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53131.23130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.88130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.05630. 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 0999 V2000\n -2.24570.81880. C 0 0 0 0 0
0 0 0 0 0 0 0\n -2.2457 -0.00630. C 0 0 0 0 0 0 0
0 0 0 0 0\n -1.5313 -0.41880. C 0 0 0 0 0 0 0 0 0
0 0 0\n -0.8168 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0
0\n -0.81680.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.10231.23130. O 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53131.23130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.88130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.05630. 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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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
Re: [Jmol-users] Jmol usually not displaying molecule
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 0999 V2000\n4.35080.48410. C 0 0 0
0 0 0 0 0 0 0 0 0\n3.63630.07160. C 0 0 0 0 0 0
0 0 0 0 0 0\n3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0
0 0 0\n4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0
0\n5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0\n5.7797
0.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n5.7797 -1.1660
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n6.4942 -0.75350.
C 0 0 0 0 0 0 0 0 0 0 0 0\n6.49420.07160. C 0 0
0 0 0 0 0 0 0 0 0 0\n6.49421.72160. C 0 0 0 0 0
0 0 0 0 0 0 0\n5.77971.30910. C 0 0 0 0 0 0 0 0
0 0 0 0\n7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0
0\n7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0\n7.6212
-0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0\n8.4181 -0.4439
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n3.9383 -1.88040.
C 0 0 0 0 0 0 0 0 0 0 0 0\n4.7633 -1.88040. C 0 0
0 0 0 0 0 0 0 0 0 0\n7.92311.72160. O 0 0 0 0 0
0 0 0 0 0 0 0\n5.06530.89660. C 0 0 0 0 0 0 0 0
0 0 0 0\n5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0
0\n5.7797 -0.34090. 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 0999
V2000\n -2.24570.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.5313
-0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.8168
-0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.81680.8188
0. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.10231.23130.
O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53131.23130. C 0 0
0 0 0 0 0 0 0 0 0 0\n -1.53132.88130. C 0 0 0 0 0
0 0 0 0 0 0 0\n -1.53132.05630. 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
0999 V2000\n -2.24570.81880. C 0 0 0 0 0 0 0
0 0 0 0 0\n -2.2457
Re: [Jmol-users] Jmol usually not displaying molecule
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 -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
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 0999 V2000 4.35080.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 3.63630.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0 7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0 8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0 3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -0.34090. 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 -- 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
Re: [Jmol-users] Jmol usually not displaying molecule
Forgot to mention this was with Safari 4.0.4. Pretty much the same behavior in Firefox 3.5.6. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** On Jan 13, 2010, at 10:24 PM, Jeff Hansen wrote: 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 0999 V2000 4.35080.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 3.63630.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 3.6363 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 4.3508 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0 6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0 6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0 5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0 7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0 6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0 7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0 8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0 3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0 7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0 5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0 5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0 5.7797 -0.34090. 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 -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating
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 0999 V2000\n4.35080.48410. C 0
0 0 0 0 0 0 0 0 0 0 0\n3.63630.07160. C 0 0 0
0 0 0 0 0 0 0 0 0\n3.6363 -0.75350. C 0 0 0 0 0
0 0 0 0 0 0 0\n4.3508 -1.16600. C 0 0 0 0 0 0 0
0 0 0 0 0\n5.0653 -0.75350. C 0 0 0 0 0 0 0 0 0
0 0 0\n5.06530.07160. C 0 0 0 0 0 0 0 0 0 0 0
0\n5.77970.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.7797 -1.16600. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.4942 -0.75350. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.49420.07160. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.49421.72160. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.77971.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.20870.48410. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.20871.30910. C 0 0 0 0 0 0 0 0 0 0 0 0\n
6.9067 -0.64290. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.6212 -0.23040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
8.4181 -0.44390. C 0 0 0 0 0 0 0 0 0 0 0 0\n
3.9383 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
4.7633 -1.88040. C 0 0 0 0 0 0 0 0 0 0 0 0\n
7.92311.72160. O 0 0 0 0 0 0 0 0 0 0 0 0\n
5.06530.89660. C 0 0 0 0 0 0 0 0 0 0 0 0\n
5.0653 -1.57850. H 0 0 0 0 0 0 0 0 0 0 0 0\n
5.7797 -0.34090. 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 -2.24570.81880. C 0 0 0 0 0 0 0 0 0 0
0 0\n -2.2457 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0
0\n -1.5313 -0.41880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.8168 -0.00630. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.81680.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-0.10231.23130. O 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53131.23130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.88130. C 0 0 0 0 0 0 0 0 0 0 0 0\n
-1.53132.05630. 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
