[Jmol-users] question about conversion of Jmol to JSmol with Java2Script
Hi folks, Your development of JSmol has inspired me to try to convert one of my own applets into JavaScript. However, my applet imports javax.swing.* and java.awt.* classes, and the developer of Java2Script says that it does not provide a Swing library. Did you encounter this problem when developing JSmol, and if so, how did you resolve it? -- Bob Grossman -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60134071iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux
I downloaded the new Jmol2.js file you gave me, and it works great! Thanks. So with this new JSmol, all the Java is now running server-side, is that correct? I no longer have to worry about whether the user's Java is enabled? From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Mon, 23 Sep 2013 22:18:28 -0500 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux There may be a few differences like that. For now, just use Jmol.script(yourAppid, 'load DATA mydata\n' + yourInlineData + '\nEND mydata ') or give this one a try: http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B robert.gross...@uky.edumailto:robert.gross...@uky.edu wrote: OK, I read a little further down in the Wiki and saw that I could accomplish the switch another way: leave the calls to jmolApplet(), etc. alone and instead use both JSmol.min.js and Jmol2.js as resources. So I did so, and I also added a symlink to the jsmol/j2s folder in the same folder as the page that calls the applet. So now JSmol loads, but I get this alert: jmolLoadInline not implemented So, any chance of this method being implemented in the near future? Or maybe it has already been implemented in a more recent version? I'm using jsmol-13.3.4. (BTW, I tried to download JSmol 13.3.5 from SourceForge, but decompression failed. Instead I downloaded one of the 13.3.4 versions.) -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux
Maciek, So you need Java running on the client, but not enabled in the browser. Is that right? -- Bob G. From: Maciek Wójcikowski mac...@wojcikowski.plmailto:mac...@wojcikowski.pl Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Tue, 24 Sep 2013 15:56:34 +0200 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux Both Java and JavaScript are computed on client side. The huge difference is that, as you mentioned, there's no need for Oracle Java plugin any more - every bit of JavaScript runs in the browser. Pozdrawiam, | Best regards, Maciek Wójcikowski mac...@wojcikowski.plmailto:mac...@wojcikowski.pl 2013/9/24 Grossman, Robert B robert.gross...@uky.edumailto:robert.gross...@uky.edu I downloaded the new Jmol2.js file you gave me, and it works great! Thanks. So with this new JSmol, all the Java is now running server-side, is that correct? I no longer have to worry about whether the user's Java is enabled? From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Date: Mon, 23 Sep 2013 22:18:28 -0500 To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol -- part deux There may be a few differences like that. For now, just use Jmol.script(yourAppid, 'load DATA mydata\n' + yourInlineData + '\nEND mydata ') or give this one a try: http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B robert.gross...@uky.edumailto:robert.gross...@uky.edu wrote: OK, I read a little further down in the Wiki and saw that I could accomplish the switch another way: leave the calls to jmolApplet(), etc. alone and instead use both JSmol.min.js and Jmol2.js as resources. So I did so, and I also added a symlink to the jsmol/j2s folder in the same folder as the page that calls the applet. So now JSmol loads, but I get this alert: jmolLoadInline not implemented So, any chance of this method being implemented in the near future? Or maybe it has already been implemented in a more recent version? I'm using jsmol-13.3.4. (BTW, I tried to download JSmol 13.3.5 from SourceForge, but decompression failed. Instead I downloaded one of the 13.3.4 versions.) -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson Larson-Anderson Professor of Chemistry St. Olaf College Northfield, MN http://www.stolaf.edu/people/hansonr 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 -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/jmol-users -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors
[Jmol-users] switching to JSmol
Amjad,
I have switched from Jmol Java applet to JSmol. It was very easy.
(1) After downloading JSmol into a folder called jsmol, I put a symlink to it
in a folder in my application, called /nosession.
(2) I changed every instance of
script src=/nosession/jsmol/Jmol.js type=text/javascript/script
in my application to
script src=/nosession/jsmol/JSmol.min.js type=text/javascript/script
script src=/nosession/jsmol/Jmol2.js type=text/javascript/script
The order of these two resources was important.
(3) In Jmol2.js, I changed
Jmol.Info = {
jarPath: java,
jarFile: ,
j2sPath: j2s,
to
Jmol.Info = {
jarPath: /nosession/jsmol/java,
jarFile: ,
j2sPath: /nosession/jsmol/j2s,
That's all it took. The only problem I encountered was that one of the Jmol
methods I was using, jmolLoadInline(), we not yet implemented in Jmol2.js. Bob
Hanson kindly provided me with a fresh version of Jmol2.js that had the method.
-- Bob G.
From: Amjad Farooq am...@farooqlab.netmailto:am...@farooqlab.net
Reply-To:
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Tue, 24 Sep 2013 10:26:34 -0400
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol --
part deux
Hi Robert,
I am utterly confused now. What is this Jmol2.js? Are you saying that using
this file one can run Jmol on the client machine even if it does not have a
Java installed? In other words, Jmol2.js runs Java from the server side? Is
that correct?
Can someone please elaborate on this point. I recently switched to JSmol simply
because many of my collaborators complained about my Jmol interface not running
on their machines due to Java issues. Now, if Jmol2.js can eliminate the need
for client to have a fully functional Java, then why do I need to to switch to
JSmol?
I am lost on this.
Amjad
AMJAD FAROOQ PhD DIC | Associate Professor
Dept of Biochemistry Molecular Biology | Miller School of Medicine |
University of Miami | Miami | FL 33136
Located @ Gautier Building #217 | Mail @ 1011 NW 15th Street #217, Miami , FL
33136
am...@farooqlab.netmailto:am...@farooqlab.net | off 305-243-2429 | lab
305-243-9799 | fax 305-243-3955 | www.farooqlab.nethttp://www.farooqlab.net
On Tue, Sep 24, 2013 at 9:49 AM, Grossman, Robert B
robert.gross...@uky.edumailto:robert.gross...@uky.edu wrote:
I downloaded the new Jmol2.js file you gave me, and it works great! Thanks.
So with this new JSmol, all the Java is now running server-side, is that
correct? I no longer have to worry about whether the user's Java is enabled?
From: Robert Hanson hans...@stolaf.edumailto:hans...@stolaf.edu
Reply-To:
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Date: Mon, 23 Sep 2013 22:18:28 -0500
To: jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
jmol-users@lists.sourceforge.netmailto:jmol-users@lists.sourceforge.net
Subject: Re: [Jmol-users] difficulties encountered in switching to JSmol --
part deux
There may be a few differences like that. For now, just use
Jmol.script(yourAppid, 'load DATA mydata\n' + yourInlineData + '\nEND
mydata ')
or give this one a try:
http://chemapps.stolaf.edu/jmol/jsmol/js/Jmol2.js
On Mon, Sep 23, 2013 at 3:15 PM, Grossman, Robert B
robert.gross...@uky.edumailto:robert.gross...@uky.edu wrote:
OK, I read a little further down in the Wiki and saw that I could accomplish
the switch another way: leave the calls to jmolApplet(), etc. alone and instead
use both JSmol.min.js and Jmol2.js as resources. So I did so, and I also added
a symlink to the jsmol/j2s folder in the same folder as the page that calls the
applet. So now JSmol loads, but I get this alert:
jmolLoadInline not implemented
So, any chance of this method being implemented in the near future? Or maybe
it has already been implemented in a more recent version? I'm using
jsmol-13.3.4. (BTW, I tried to download JSmol 13.3.5 from SourceForge, but
decompression failed. Instead I downloaded one of the 13.3.4 versions.)
--
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--
Robert M. Hanson
Larson-Anderson Professor of Chemistry
St. Olaf College
Northfield, MN
http://www.stolaf.edu/people/hansonr
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah
[Jmol-users] difficulties encountered in switching to JSmol -- advice please?
Hi all,
I am looking at switching from Jmol to JSmol. The WIki page says ,
Modifying function calls from the format jmolXxxx(..., appletExtension) to
Jmol.jmolXxxx(appletID, ...)
So I have done that, and I am seeing undefined methods errors in the error
console:
TypeError: 'undefined' is not a function (evaluating
'Jmol.jmolInitialize('../nosession/jsmol')')
TypeError: 'undefined' is not a function (evaluating 'Jmol.jmolApplet([width,
height], jmolStartScript, jmolNum)')
Are these methods not supported in JSmol? Are there workarounds?
Here are the methods that I have used to initiate and run Jmol in the past. I
have a js page with the following code:
var jmolMols = new Array();
var addlScripts = new Array();
function setJmol(jmolNum, jmolMol, bgcolor, width, height, addlScript) {
jmolMols[jmolNum] = jmolMol;
addlScripts[jmolNum] = addlScript;
var jmolStartScript = 'background ' + bgcolor
+ '; javascript jmolLoaded(' + jmolNum + '); ';
jmolApplet([width, height], jmolStartScript, jmolNum);
} // setJmol()
// this method will be called after the applet initialization is complete
function jmolLoaded(jmolNum) {
jmolLoadInline(jmolMols[jmolNum], jmolNum);
jmolScript(addlScripts[jmolNum], jmolNum);
} // jmolLoaded()
setJmol() is called by this script in the HTML, where I want the applet to
appear:
script type=text/javascript
// !-- % %
setJmol(%= jmolNum %,
'%= Utils.toValidJS(
figData[Figure.STRUCT]) %',
'white', 250, 250,
'%= Utils.toValidJS(
figData[Figure.JMOL_SCRIPTS])
%');
// --
/script
The JSP page also has this call in its Javascript section:
Jmol.jmolInitialize('../nosession/jsmol')
-- Bob Grossman (not Bob Hanson)
--
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[Jmol-users] difficulties encountered in switching to JSmol -- part deux
OK, I read a little further down in the Wiki and saw that I could accomplish the switch another way: leave the calls to jmolApplet(), etc. alone and instead use both JSmol.min.js and Jmol2.js as resources. So I did so, and I also added a symlink to the jsmol/j2s folder in the same folder as the page that calls the applet. So now JSmol loads, but I get this alert: jmolLoadInline not implemented So, any chance of this method being implemented in the near future? Or maybe it has already been implemented in a more recent version? I'm using jsmol-13.3.4. (BTW, I tried to download JSmol 13.3.5 from SourceForge, but decompression failed. Instead I downloaded one of the 13.3.4 versions.) -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60133471iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] converting to JSmol
Hi all,
I am looking at converting from Jmol to JSmol. The WIki page says ,
Modifying function calls from the format jmolXxxx(..., appletExtension) to
Jmol.jmolXxxx(appletID, ...)
So I have done that, and I am seeing undefined methods errors in the error
console:
TypeError: 'undefined' is not a function (evaluating
'Jmol.jmolInitialize('../nosession/jsmol')')
TypeError: 'undefined' is not a function (evaluating 'Jmol.jmolApplet([width,
height], jmolStartScript, jmolNum)')
Are these methods not supported in JSmol? Are there workarounds?
Here are the methods that I have used to initiate and run Jmol in the past. I
have a js page with the following code:
var jmolMols = new Array();
var addlScripts = new Array();
function setJmol(jmolNum, jmolMol, bgcolor, width, height, addlScript) {
jmolMols[jmolNum] = jmolMol;
addlScripts[jmolNum] = addlScript;
var bgcolor = bgcolor.replace('#', 'x');
// if color has format for use in HTML style attribute
if (!isNaN(parseInt(bgcolor, 16)))
bgcolor = 'x' + bgcolor; // if color is hexadecimal without x prefix
if (bgcolor.charAt(0) == 'x')
bgcolor = '[' + bgcolor + ']'; // if color is not English
var jmolStartScript = 'background ' + bgcolor
+ '; javascript jmolLoaded(' + jmolNum + '); ';
jmolApplet([width, height], jmolStartScript, jmolNum);
} // setJmol()
// this method will be called after the applet initialization is complete
function jmolLoaded(jmolNum) {
jmolLoadInline(jmolMols[jmolNum], jmolNum);
jmolScript(addlScripts[jmolNum], jmolNum);
} // jmolLoaded()
setJmol() is called by this script in the HTML, where I want the applet to
appear:
script type=text/javascript
// !-- % %
setJmol(%= jmolNum %,
'%= Utils.toValidJS(
figData[Figure.STRUCT]) %',
'white', 250, 250,
'%= Utils.toValidJS(
figData[Figure.JMOL_SCRIPTS])
%');
// --
/script
The JSP page also has this call in its Javascript section:
Jmol.jmolInitialize('../nosession/jsmol')
-- Bob
--
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Re: [Jmol-users] revision of Jmol.js -- was Re: help displaying jvxl MO
Couldn't you do something along the lines of encodeURIComponent()? Convert all % to %25, and convert all \n and \r symbols to %0A and %0D ? On 1/24/10 5:33 PM, Robert Hanson hans...@stolaf.edu wrote: I've altered Jmol.js when it finds that a model has a vertical bar in it to substitute the string \\/n -- escaped backslash - forward slash - n -- sort of along the lines of what your server is doing. This would be a VERY unusual thing to have in a model file. (I suppose it's not impossible, so technically this is still a hack.) -- 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] revision of Jmol.js -- was Re: help displaying jvxl MO
Yes, of course it does, but the point is you look for any string beginning with % and you know it is an encoded character. Kind of like using in HTML. ChemAxon uses it to pass parameters to the Marvin applets. On 1/24/10 5:57 PM, Robert Hanson hans...@stolaf.edu wrote: JVXL includes those characters. On Sun, Jan 24, 2010 at 4:48 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Couldn't you do something along the lines of encodeURIComponent()? Convert all % to %25, and convert all \n and \r symbols to %0A and %0D ? On 1/24/10 5:33 PM, Robert Hanson hans...@stolaf.edu wrote: I've altered Jmol.js when it finds that a model has a vertical bar in it to substitute the string \\/n -- escaped backslash - forward slash - n -- sort of along the lines of what your server is doing. This would be a VERY unusual thing to have in a model file. (I suppose it's not impossible, so technically this is still a hack.) -- 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] revision of Jmol.js -- was Re: help displaying jvxl MO
I see only a blank page when I go there. I don't even see the text in the body. On 1/24/10 5:33 PM, Robert Hanson hans...@stolaf.edu wrote: I've put your file up as a sample at http://chemapps.stolaf.edu/jmol/docs/examples-11/appletInline.htm -- 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] revision of Jmol.js -- was Re: help displaying jvxl MO
Now it works. On 1/24/10 9:36 PM, Robert Hanson hans...@stolaf.edu wrote: I just forgot the // -- tag. Should be working now. On Sun, Jan 24, 2010 at 5:55 PM, Grossman, Robert B robert.gross...@uky.edu wrote: I see only a blank page when I go there. I don't even see the text in the body. On 1/24/10 5:33 PM, Robert Hanson hans...@stolaf.edu wrote: I've put your file up as a sample at http://chemapps.stolaf.edu/jmol/docs/examples-11/appletInline.htm -- 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] help displaying jvxl MO
Hi Bob,
The information is read from an Oracle database and written into a JSP page.
We have the ability to write information to files, but we want very much to
avoid having to do it. We also want to avoid having to deal with multiple
files to display a single molecule and its associated MOs. From my point of
view, Jmol's preference for loading information from files is a real drawback.
We worked around the problem by using a .mo file instead of a .jvxl file. We
were able to load the .mo file inline and display its MOs without any problem.
A friend gave us the proper Jmol JS commands to use to display the MOs.
jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No
isosurface commands.
I don't think that we could have mangled the .jvxl information because the .mo
information, which was loaded and transmitted in exactly the same way, was not
mangled. But I could be wrong.
So is it correct that we use isosurface to load MOs into Jmol, and we use
mo to induce Jmol to display them?
-- Bob
On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:
Well, two things. First, you must have mangled the data some way - or at least
clipping from this page doesn't work. Because the attached file did run.
Second, you can only load an isosurface inline like that in the very latest
version of Jmol. (I'm not sure it's even in the one I have up at
http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here)
isosurface INLINE @{javascript(getMol())}
that tells Jmol to read the output of the JavaScript getMol() function as the
data for the isosurface instead of reading the data from a file.
Any reason you don't want to have that data in a file? -- or is this coming
back from a server and you are trying to keep it all together? Sure would be
simpler:
isosurface somefile.jvxl
Bob
On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B robert.gross...@uky.edu
wrote:
Hi,
I have a JVXL file containing MO data that I am trying to display. I can see
the molecule, but I can't see the MO. I have tried various scripts to turn on
the MO, to no avail. Below I have copied the relevant part of my Web page. I
am using 'mo HOMO;' as the script, but I have tried several other commands,
including none, to no avail. How do I display the MO? Does the fact that I
load inline prevent the MO from being displayed?
-- Bob
script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638,
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:
--
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] help displaying jvxl MO
We can let Jmol create the MO from the QM data in the browser - I think that is
what we are doing now with the .mo file - but we greatly prefer to read the QM
data from the database, not from a file.
I'm still trying to understand the mutual dependencies among load, isosurface,
and mo.
When I use jmolLoadInline() with the contents of the .mo file, I can see the
structure, and I can use the script mo (as implemented by the jmolMenu() JS
command) to display the MOs.
When I use jmolLoadInline() with the contents of the .jvxl file, I can see
the structure, but I cannot find a script that will display the isosurface. Is
there a script that will display the isosurface after I load it into Jmol with
jmolLoadInline()?
On 1/23/10 8:39 PM, Robert Hanson hans...@stolaf.edu wrote:
I think it just got mangled as being part of the email.
isosurface is used to create MOs from files that are not QM files. -- surfaces.
mo is used to generate the MO data directly from the basis functions. Most
people these days, I think, just let Jmol read the QM file and create the MO in
the browser -- no need for a server end. Are you certain you can't do that?
Bob
On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B robert.gross...@uky.edu
wrote:
Hi Bob,
The information is read from an Oracle database and written into a JSP page.
We have the ability to write information to files, but we want very much to
avoid having to do it. We also want to avoid having to deal with multiple
files to display a single molecule and its associated MOs. From my point of
view, Jmol's preference for loading information from files is a real drawback.
We worked around the problem by using a .mo file instead of a .jvxl file. We
were able to load the .mo file inline and display its MOs without any problem.
A friend gave us the proper Jmol JS commands to use to display the MOs.
jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No
isosurface commands.
I don't think that we could have mangled the .jvxl information because the .mo
information, which was loaded and transmitted in exactly the same way, was not
mangled. But I could be wrong.
So is it correct that we use isosurface to load MOs into Jmol, and we use
mo to induce Jmol to display them?
-- Bob
On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote:
Well, two things. First, you must have mangled the data some way - or at least
clipping from this page doesn't work. Because the attached file did run.
Second, you can only load an isosurface inline like that in the very latest
version of Jmol. (I'm not sure it's even in the one I have up at
http://chemapps.stolaf.edu) What you would need to do is (all Jmol script here)
isosurface INLINE @{javascript(getMol())}
that tells Jmol to read the output of the JavaScript getMol() function as the
data for the isosurface instead of reading the data from a file.
Any reason you don't want to have that data in a file? -- or is this coming
back from a server and you are trying to keep it all together? Sure would be
simpler:
isosurface somefile.jvxl
Bob
On Wed, Jan 20, 2010 at 3:27 PM, Grossman, Robert B robert.gross...@uky.edu
wrote:
Hi,
I have a JVXL file containing MO data that I am trying to display. I can see
the molecule, but I can't see the MO. I have tried various scripts to turn on
the MO, to no avail. Below I have copied the relevant part of my Web page. I
am using 'mo HOMO;' as the script, but I have tried several other commands,
including none, to no avail. How do I display the MO? Does the fact that I
load inline prevent the MO from being displayed?
-- Bob
script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638,
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type:
--
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
Re: [Jmol-users] help displaying jvxl MO
Ah, I see. And the .jvxl file that my friend sent me must have been created by Jmol from a QM calculation that my friend had generated with WebMO and loaded into Jmol. So when he was trying to make my life easier by sending me the .jvxl file instead of the WebMO results file, he was really making it more difficult, because I was loading the data inline, and Jmol couldn't read the isosurface data in the .jvxl file. It all becomes much clearer now... It seems the best solution for us is just to store the QM results file into the database, deliver the data inline to Jmol, and use scripts and the Javascript library to have Jmol generate the MOs. It achieves all our goals. Thanks for your patient explanations. On 1/23/10 11:34 PM, Robert Hanson hans...@stolaf.edu wrote: On Sat, Jan 23, 2010 at 9:33 PM, Grossman, Robert B robert.gross...@uky.edu wrote: We can let Jmol create the MO from the QM data in the browser - I think that is what we are doing now with the .mo file - but we greatly prefer to read the QM data from the database, not from a file. I'm still trying to understand the mutual dependencies among load, isosurface, and mo. When I use jmolLoadInline() with the contents of the .mo file, I can see the structure, and I can use the script mo (as implemented by the jmolMenu() JS command) to display the MOs. By .MO file, not sure what you mean there, unless that's a WebMO file. The fact that you can use the MO command indicates that you are creating the orbitals from the basis functions and coefficients. When I use jmolLoadInline() with the contents of the .jvxl file, I can see the structure, but I cannot find a script that will display the isosurface. Is there a script that will display the isosurface after I load it into Jmol with jmolLoadInline()? This older JVXL file format was modeled on the CUBE format and thus did save up to the first 100 atoms; the newer XML version doesn't. But all you are doing there is reading the atoms. The load command doesn't read any surfaces ever. If the file has QM basis and coefficients, then those are read at load time (and the popup menu will be populated with items showing all the orbitals and their energies). The JVXL file is really a surface file and is read using the ISOSURFACE command. Until last week you couldn't load those inline. (You could load PMESH data -- simple triangles -- inline, but you couldn't use the isosurface INLINE keyword with anything else. I think I changed that early last week. So if that's really what you want to do, you need to use Jmol 11.9.21. So you can load MO data two ways -- with the LOAD/MO command combination or with the ISOSURFACE command. In Jmol MO is a subset of ISOSURFACE so the same code is run, but the options are a bit different. When you use MO homo you get a basic, standard orbital, with a nice listing of orbital properties in the upper left corner. Options are pretty much limited to cutoff and color. With ISOSURFACE MO homo you don't get that listing, but you have a bit more flexibility -- you can, for example, choose to ignore atoms and only see contributions from a subset, and you can do contouring, planar slices, topo maps, and such. I need to get this into the documentation Bob On 1/23/10 8:39 PM, Robert Hanson hans...@stolaf.edu wrote: I think it just got mangled as being part of the email. isosurface is used to create MOs from files that are not QM files. -- surfaces. mo is used to generate the MO data directly from the basis functions. Most people these days, I think, just let Jmol read the QM file and create the MO in the browser -- no need for a server end. Are you certain you can't do that? Bob On Sat, Jan 23, 2010 at 6:08 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi Bob, The information is read from an Oracle database and written into a JSP page. We have the ability to write information to files, but we want very much to avoid having to do it. We also want to avoid having to deal with multiple files to display a single molecule and its associated MOs. From my point of view, Jmol's preference for loading information from files is a real drawback. We worked around the problem by using a .mo file instead of a .jvxl file. We were able to load the .mo file inline and display its MOs without any problem. A friend gave us the proper Jmol JS commands to use to display the MOs. jmolMenu([['mo delete;','none'],['mo 3',3],['mo 4',4] ...]); . No isosurface commands. I don't think that we could have mangled the .jvxl information because the .mo information, which was loaded and transmitted in exactly the same way, was not mangled. But I could be wrong. So is it correct that we use isosurface to load MOs into Jmol, and we use mo to induce Jmol to display them? -- Bob On 1/23/10 5:44 PM, Robert Hanson hans...@stolaf.edu wrote: Well, two things. First, you must have mangled the data some way - or at least clipping
[Jmol-users] help displaying jvxl MO
Hi,
I have a JVXL file containing MO data that I am trying to display. I can see
the molecule, but I can't see the MO. I have tried various scripts to turn on
the MO, to no avail. Below I have copied the relevant part of my Web page. I
am using 'mo HOMO;' as the script, but I have tried several other commands,
including none, to no avail. How do I display the MO? Does the fact that I
load inline prevent the MO from being displayed?
-- Bob
script type=text/javascript
// !--
function getMol() {
return '#JVXL VERSION 1.4\n#created by Jmol Version 11.6.15 2008-11-24
13:39 on Wed Dec 09 20:51:19 CST 2009\nMO range (-4.286028, -4.170638,
-6.45537) to (5.6358566, 10.584962, 3.6056142)\ncalculation type: ?\n-32
-4.286028 -4.170638 -6.45537 ANGSTROMS\n80 0.12402356 0.0 0.0\n80 0.0 0.184445
0.0\n80 0.0 0.0 0.1257623\n6 6.0 0.0 0.0 0.0\n6 6.0 1.5335295 0.0 0.0\n8 8.0
2.447 1.1734227 0.0\n6 6.0 2.3022442 2.08224 -1.0298198\n6 6.0 1.9440373
3.352165 -0.783915\n6 6.0 2.166842 4.391685 -1.8063345\n8 8.0 1.4540279
5.5320063 -1.5695299\n6 6.0 1.4419276 6.5410266 -2.576349\n6 6.0 0.4292079
7.5804462 -2.13194\n1 1.0 0.699213 8.036855 -1.1707217\n1 1.0 0.36370665
8.384962 -2.8751543\n1 1.0 -0.57431144 7.149238 -2.0169382\n1 1.0 2.4541469
6.9775352 -2.6722505\n1 1.0 1.1674224 6.103718 -3.555268\n8 8.0 2.9358563
4.365084 -2.7551525\n1 1.0 1.4746284 3.6545703 0.16250335\n1 1.0 2.660351
1.708333 -1.9975383\n6 6.0 2.025939 -0.95221835 -1.101621\n1 1.0 1.6514318
-1.9706379 -0.937718\n1 1.0 1.6784323 -0.62881225 -2.0926402\n1 1.0 3.1216602
-1.0091194 -1.1394216\n1 1.0 1.869836 -0.3798073 0.9982192\n6 6.0 -0.86121655
0.62561214 -1.0898211\n6 6.0 -0.8380163 2.0938404 -1.2457241\n6 6.0 -0.81681573
2.6353507 -2.5209484\n7 7.0 -0.79011524 3.084059 -3.6053698\n6 6.0 -1.1576223
2.898656 -0.16150327\n7 7.0 -1.4360279 3.5764692 0.75561434\n1 1.0 -0.59091145
0.1594031 -2.0609396\n1 1.0 -1.9027367 0.2891056 -0.885317\n1 1.0 -0.29010567
-1.0688207 0.08750176\n1 1.0 -0.314506 0.47200906 0.95541835\n-1 35 90 35 90
Jmol voxel format version 1.4\n# \n0.05 361 -1362 1362 -1.0 1.0 -1.0 1.0
rendering:isosurface ID homop fill noMesh noDots notFrontOnly frontlit\n
117879 5 75 6 74 5 6154 7 72 9 71 9 71 9 72 7 75 3 5915 7 72 9 70 11 69 11 69
11 70 10 71 7 5834 4 74 9 70 11 68 13 67 13 67 13 68 12 69 9 73 5 5754 7 71 11
68 13 67 13 66 14 67 13 67 13 68 11 71 7 5752 8 71 11 68 13 66 14 66 15 65 15
66 13 68 11 71 7 334 2 77 4 77 2 5256 8 70 12 68 13 66 14 66 14 66 14 67 13 68
11 71 7 173 3 75 6 74 7 72 8 73 6 75 4 5176 8 71 11 68 12 67 14 66 14 66 14 67
12 69 10 73 4 173 6 73 8 71 10 70 9 72 8 73 6 5176 6 72 10 69 11 69 12 68 12 68
11 70 9 73 5 175 2 75 7 72 9 71 10 70 10 70 9 72 7 5256 6 72 9 71 9 71 9 72 7
75 2 256 3 75 7 72 9 71 9 71 9 71 9 72 7 5993 7 72 9 71 9 71 9 71 8 74 5 5801 4
74 7 73 7 29 5 39 7 28 7 40 4 28 8 73 7 73 6 5800 5 74 7 72 9 71 9 71 9 28 4 40
7 29 5 75 5 77 1 4709 4 77 3 1008 7 72 9 70 10 70 10 71 9 72 7 75 3 4743 3 76 5
75 5 77 3 928 7 72 9 70 10 70 10 71 9 72 7 75 3 4742 4 76 5 75 5 76 4 928 6 73
8 71 10 70 10 71 9 72 7 4820 3 77 5 75 5 76 4 929 4 75 7 72 8 72 8 73 7 74 5
4822 1 78 4 76 4 77 3 1010 5 74 6 74 6 75 5 4982 2 78 2
279630\nW4?A7Kv(0Dwm)s(RKaX!S@V0QmxtbS9C3Omxtb9B|#HVR:PQ|RBGbHJB!-8:#vKSHeHZQ`a...@tu(DQOaJ[6OJRKgiv\'trpm+r...@f7ob*7gzt4@dX!q:`...@ag|ga{$l{\'-v9-wuv+p2wm...@[s7k]u[Fw,*\'Lq##%$l|R-5pEO=W?69JmAOWTW\'_XQcN[n*cJOw\'m31X,GNHDmuXy^Izv+kA2axMh_lP:ZqF1*-!,lA;p.)w*)E8BQXQleUe,Z60]Nrx[zeCzs(b;23c`]buFGwJ6\/3cg...@a`tvvjk4dj4:,+eS\'c\'e5j-mMYzUSYS*ES9Xc^Hj9!cv|wgBP74=JC\'+g^uny...@kon^c:I2*w,@re=YqVOVpfMXiEKqP2Tntyt{_e125nBUkx4btL\'^\'tFOE{#YXCwPuT[HX|;8XXq*P]T\/O4;9TBwZPXsOS.STEk,e*rMsrUZOT^]s.d7GeQvLo8KU!4ql(*(drzx]gjazd...@g8kn@FWtce=9e2^F;CSlmC.(\/ErmVLLSazymkrw+OcjfT\/H6A]^LK+v#w=Q45JQM,UG`631[smx\/9\'-\']3h\'g9{EKKwDX7t\'y#P^baZLp4S^+DXejjbR6Qx$R^ecZF##uk(=JOK=%x|m)\/K6![mrm[4TINK2tJrk|pN0G()UDG)N#y.7cro?(3N?QDKA:5m!){Wl{yxfSHnw\/BcymJ!Zd-X_ma0_Za6)s46n+]z=eap0dabuyll+gc`e99d].itfk...@lqvz)3$xJgwBoIiIC:WTZ;.`\/[;[%o%\/1.1$$)9S4]Yr{pXu2;@^=FxUl^Jh0rFC6VA]Ca;A3B\/u!dz%.rz7L[`=LdD2))1Dfa1ZFI8P-e(kr-tJc;^rH%|#g$$#8O;In3.;ibxkw)h...@]lqnd\/GICGPinIc!MXjn.bD(Q7Bb[=q]W1%`*45Zz!A1))0a`l...@%w8p$9xr,vxM.MsTf(8\'x#=YN_];G[vysz96LWZVJ5VT.wqH^r:dd2x7N9sRHX-9[OiXX+tjb0C?EfL44;Ll{v{jisss1NEPSN@(0HCpc4=_JFE[)u;K*9Qv9oKovNQxE|,dD[|bRJIReI,T8;4$\'l#T#rgBYT\'x|diBN^FGWn`HQaA9p7IrX1j:iC|*6N1DStklvgLFUz)F,^jlfU7NFw6ixct+;6qXN0-k7RG[K733z%HXj7W;uxg...@zmpfl++n\/\/6`j(S.tiBS;9qARHJ\/3`8gs...@wkt8hpdf.\/*);_]snyS6($+?aU+OAqyiF4bJ|m\'R`{3YB5ahgED38-C1gBbhXS[o|]MHOap]X^q\n|~1361
\n#---end of jvxl file data---\n# cutoff = 0.05; pointsPerAngstrom =
8.062984; nSurfaceInts = 361; nBytesData = 3736; bicolor map\n# created using
Jvxl.java\n# precision: false nColorData 1362\n# isosurface homop cutoff +0.05
mo homo fill;\n# isosurface ID homop fill noMesh noDots notFrontOnly
frontlit\n# bytes read: 0; approximate voxel-only input\/output byte ratio:
[Jmol-users] browser hanging again
Hi, Jmol is consistently hanging my browser (Safari and Firefox both) when I display a particular page. It's a page in which I display a list of 13 questions. The page contains about one figure per question, all of which are JPEGs, except one question has a Jmol applet. However, when I display a page with a list of 3 questions, the browser does not hang. I'm showing the same Jmol content (or nearly so) in the two pages. The only difference between the two pages that I can see is that in the one that hangs, the Jmol applet is off the end of the screen. I can't imagine that would be enough to make Jmol hang, but maybe I'm wrong. The HTML of the two pages is posted at http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp1.txt (doesn't crash the browser) and http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp2.txt (crashes the browser). Search for jmolApplet to find the call to Jmol. Any insight you could offer would be appreciated. -- Bob G. -- 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] Marvin Sketch
Do you mean that you want to draw a structure in Marvin and press a button to send it to Jmol? I can probably put one together over the weekend, if no one has one ready. From: Robert Hanson hans...@stolaf.edu Reply-To: jmol-users@lists.sourceforge.net Date: Fri, 15 Jan 2010 14:01:20 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Marvin Sketch Subject: [Jmol-users] Marvin Sketch Does anyone have a page that we can play with that would allow Marvin input of 2D structures and Jmol rendering of them in 3D? -- 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] could not find applet jmolApplet0
This one's not a hanging offense, but I started using script tags for my Jmol
applets because I may have more than one per page, and each time I load a page
now, I get an alert saying, could not find applet jmolApplet0. It appears to
be of no consequence, because the applets, whether there's one or more, load
fine. At first I was naming my applets jmolApplet1, jmolAppet2, etc., so I
changed them to jmolApplet0, etc., but I still get the message.
Here's the relevant part of the code:
script type=text/javascript
var jmolMol0 = '\n Marvin 03180516593D\n\n 22
22 0 0 0 0999 V2000\n -0.42010.2577 -1.4146 C 0 0 0
0 0 0 0 0 0 6 0 0\n1.01190.6024 -0.9257 C 0 0 2 0 0 0
0 0 0 5 0 0\n1.4430 -0.31570.2489 C 0 0 2 0 0 0 0 0 0
4 0 0\n0.4201 -0.25771.4146 C 0 0 0 0 0 0 0 0 0 3 0
0\n -1.0119 -0.60240.9257 C 0 0 0 0 0 0 0 0 0 2 0 0\n
-1.44300.3157 -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\n1.72070.5093
-1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0\n1.5221 -1.3462 -0.1098
H 0 0 0 0 0 0 0 0 0 0 0 0\n0.7193 -0.94602.2082 H 0 0
0 0 0 0 0 0 0 0 0 0\n0.42120.74821.8450 H 0 0 0 0 0
0 0 0 0 0 0 0\n -1.7207 -0.50931.7516 H 0 0 0 0 0 0 0 0
0 0 0 0\n -1.0386 -1.64540.5961 H 0 0 0 0 0 0 0 0 0 0 0
0\n -1.52211.34620.1098 H 0 0 0 0 0 0 0 0 0 0 0 0\n
-2.43310.0241 -0.6065 H 0 0 0 0 0 0 0 0 0 0 0 0\n2.8389
0.09540.7531 C 0 0 0 0 0 0 0 0 0 0 0 0\n1.04952.0704
-0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0\n2.38322.8404
-0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.27422.8574 -0.4618
C 0 0 0 0 0 0 0 0 0 0 0 0\n4.1725 -0.67460.7531 C 0 0
0 0 0 0 0 0 0 0 0 0\n5.4409 -0.01771.3286 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';
var bgcolor = 'white';
var height = 250;
var width = 250;
var addlScripts = 'set spin y 20; ';
/script
!-- method for displaying Jmol,
http://jmol.sourceforge.net, in a jsp page
* Java variables must be defined in the host page:
* String pathToRoot
* String jmolJSCmds (semicolon-separated list of commands from Jmol
Javascript library,
* http://jmol.sourceforge.net/jslibrary/ )
* int jmolNum
* JS variables must be defined in the host page:
* string variables jmolMol0, bgcolor, addlScripts (semicolon-separated
list
* of Jmol scripting commands)
* int variables width, height
* Use lt;%@ include page= %gt; in the host page.
--
script type=text/javascript
// !--
function jmolLoaded0() {
jmolLoadInline(jmolMol0, 'jmolApplet0');
jmolScript(addlScripts);
}
jmolInitialize('../nosession/jmol');
bgcolor = bgcolor.replace(/#/g, 'x'); // if color has format of HTML tags
if (!isNaN(parseInt(bgcolor, 16))) bgcolor = 'x' + bgcolor; // if color is
hexadecimal only
if (bgcolor.charAt(0) == 'x') bgcolor = '[' + bgcolor + ']'; // if color is
not English
var jmolStartScript = 'background ' + bgcolor
+ '; javascript jmolLoaded0(); ';
jmolApplet([width, height], jmolStartScript, 'jmolApplet0');
// --
/script
--
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] browser hanging again
Bob, your late-night efforts appear not to have been in vain. With the Jmol-11.zip folder you reference below, my browser no longer crashes. I did not even use the ?JMOLJAR formulation in my URL. Let's hope you've solved the problem for good now. -- Bob On 1/15/10 7:28 PM, Robert Hanson hans...@stolaf.edu wrote: Ah, OK. I spent almost all last night (I mean ALL) fixing this nasty bug. I introduced it into both Jmol 11.8 and 11.9 last month, I'm afraid. Should be fixed in Jmol 11.8.17 and Jmol 11.9.19, both ready for release. Please try the Jar files in http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol-11.zip and see if that fixes it. You can do this by using your link with the following appended: ?JMOLJAR=http://chemapps.stolaf.edu/jmol/docs/examples-11/JmolAppletSigned.jar Or at least that might work. Also, please send the link that crashes. Always fun to try to fix those. not. Bob On Fri, Jan 15, 2010 at 3:37 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, Jmol is consistently hanging my browser (Safari and Firefox both) when I display a particular page. It's a page in which I display a list of 13 questions. The page contains about one figure per question, all of which are JPEGs, except one question has a Jmol applet. However, when I display a page with a list of 3 questions, the browser does not hang. I'm showing the same Jmol content (or nearly so) in the two pages. The only difference between the two pages that I can see is that in the one that hangs, the Jmol applet is off the end of the screen. I can't imagine that would be enough to make Jmol hang, but maybe I'm wrong. The HTML of the two pages is posted at http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp1.txt (doesn't crash the browser) and http://epoch.chem.uky.edu/epoch-plugin/public/questionsList.jsp2.txt (crashes the browser). Search for jmolApplet to find the call to Jmol. Any insight you could offer would be appreciated. -- Bob G. -- 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
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.
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[Jmol-users] minor menu bug
If I control-click on the Jmol applet to bring up a menu, then try to close it by clicking on the red button on the upper left, the button has no effect. The only way to close the menu is to click on the applet again. -- 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
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
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] minor menu bug
It's a Mac thing. Three buttons, red, yellow, and green, appear on the upper left above the menu. Normally the red button closes it, the yellow button minimizes it, the green button maximizes it. From: Angel Herráez angel.herr...@uah.es Reply-To: jmol-users@lists.sourceforge.net Date: Thu, 14 Jan 2010 12:51:50 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] minor menu bug Subject: Re: [Jmol-users] minor menu bug Sorry Bob, what red button? The applet hasn't got such -- 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
[Jmol-users] background color JS error
When I sent the script background [white] to Jmol, it not only failed to run, but it prevented further execution of Javascript commands. I suggest that you accept JS names for colors, but even if you don't, I suggest that you avoid throwing JS errors by checking that the value is in an acceptable format. -- 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
[Jmol-users] feature suggestions
(1) Display H atoms. If I load a structure that does not show H atoms, it would be nice to have Jmol calculate their positions and display them. I know it must know that they are there, because when I loaded a structure with a planar C the the center of an isopropyl group, then minimized the structure, it converted the C to tetrahedral. (I guess it's possible you have this feature, but I'm not able to find it.) (2) Save image of the current view. The best format would be PNG. Yes, I can do a screen capture of a view with another program, but that's extra work. -- Bob -- 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] background color JS error
ah yes, that works. still, it should avoid throwing a JS error that prevents later commands from being executed. From: Paul Pillot paul.pil...@ac-orleans-tours.fr Reply-To: jmol-users@lists.sourceforge.net Date: Thu, 14 Jan 2010 14:08:22 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] background color JS error Subject: Re: [Jmol-users] background color JS error What about background white ? Jmol does accept js color names. Paul Le 14 janv. 2010 à 19:41, Grossman, Robert B a écrit : When I sent the script background [white] to Jmol, it not only failed to run, but it prevented further execution of Javascript commands. I suggest that you accept JS names for colors, but even if you don't, I suggest that you avoid throwing JS errors by checking that the value is in an acceptable format. -- 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 -- 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] background color JS error
When I had background: [white] followed by an alert, the alert failed to appear. Seems like a runtime JS error to me. From: Paul Pillot paul.pil...@ac-orleans-tours.fr Reply-To: jmol-users@lists.sourceforge.net Date: Thu, 14 Jan 2010 14:17:42 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] background color JS error Subject: Re: [Jmol-users] background color JS error I don't think it sends a javascript error neither. On my tests it only sends a jmol error via the messagecallback method when enabled. Paul Le 14 janv. 2010 à 20:12, Grossman, Robert B a écrit : ah yes, that works. still, it should avoid throwing a JS error that prevents later commands from being executed. -- 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] background color JS error
It was in a javascript command separated from the jmolscript() call.
It was in a function that was supposed to be called after Jmol loaded.
jmolApplet(250, 'background [white]; javascript jmolLoaded();');
function jmolLoaded() {
alert(mol);
}
From: Paul Pillot paul.pil...@ac-orleans-tours.fr
Reply-To: jmol-users@lists.sourceforge.net
Date: Thu, 14 Jan 2010 14:49:27 -0500
To: jmol-users@lists.sourceforge.net
Conversation: [Jmol-users] background color JS error
Subject: Re: [Jmol-users] background color JS error
Was the alert in the same jmolscript, or in a javascript command separated from
the jmolscript() call?
Le 14 janv. 2010 à 20:19, Grossman, Robert B a écrit :
When I had background: [white] followed by an alert, the alert failed to
appear. Seems like a runtime JS error to me.
From: Paul Pillot paul.pil...@ac-orleans-tours.fr
Reply-To: jmol-users@lists.sourceforge.net
Date: Thu, 14 Jan 2010 14:17:42 -0500
To: jmol-users@lists.sourceforge.net
Conversation: [Jmol-users] background color JS error
Subject: Re: [Jmol-users] background color JS error
I don't think it sends a javascript error neither. On my tests it only sends
a jmol error via the messagecallback method when enabled.
Paul
Le 14 janv. 2010 à 20:12, Grossman, Robert B a écrit :
ah yes, that works.
still, it should avoid throwing a JS error that prevents later commands from
being executed.
--
Throughout its 18-year history, RSA Conference consistently attracts the
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Re: [Jmol-users] feature suggestions
My suggestion would be that if a multiple bond is not specified, you should assume a single bond, and if a charge or radical is not specified, you should assume enough H atoms to give the atom its octet. If the user is not specifying multiple bonds, then he simply shouldn't use the function. Consider the MOL file below. Some H atoms are specified, some not. I had Jmol do a minimization, and it correctly deplanarized the isopropyl group. If it can do that, then it can easily position the H atoms. Marvin 03180516593D 22 22 0 0 0 0999 V2000 -0.42010.2577 -1.4146 C 0 0 0 0 0 0 0 0 0 6 0 0 1.01190.6024 -0.9257 C 0 0 2 0 0 0 0 0 0 5 0 0 1.4430 -0.31570.2489 C 0 0 2 0 0 0 0 0 0 4 0 0 0.4201 -0.25771.4146 C 0 0 0 0 0 0 0 0 0 3 0 0 -1.0119 -0.60240.9257 C 0 0 0 0 0 0 0 0 0 2 0 0 -1.44300.3157 -0.2489 C 0 0 0 0 0 0 0 0 0 1 0 0 -0.71930.9460 -2.2082 H 0 0 0 0 0 0 0 0 0 0 0 0 -0.4212 -0.7482 -1.8450 H 0 0 0 0 0 0 0 0 0 0 0 0 1.72070.5093 -1.7516 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5221 -1.3462 -0.1098 H 0 0 0 0 0 0 0 0 0 0 0 0 0.7193 -0.94602.2082 H 0 0 0 0 0 0 0 0 0 0 0 0 0.42120.74821.8450 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.7207 -0.50931.7516 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.0386 -1.64540.5961 H 0 0 0 0 0 0 0 0 0 0 0 0 -1.52211.34620.1098 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.43310.0241 -0.6065 H 0 0 0 0 0 0 0 0 0 0 0 0 2.83890.09540.7531 C 0 0 0 0 0 0 0 0 0 0 0 0 1.04952.0704 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0 2.38322.8404 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.27422.8574 -0.4618 C 0 0 0 0 0 0 0 0 0 0 0 0 4.1725 -0.67460.7531 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4409 -0.01771.3286 C 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 5 6 1 0 0 0 0 1 7 1 0 0 0 0 1 8 1 0 0 0 0 2 9 1 0 0 0 0 2 18 1 0 0 0 0 3 17 1 0 0 0 0 3 10 1 0 0 0 0 4 11 1 0 0 0 0 4 12 1 0 0 0 0 5 13 1 0 0 0 0 5 14 1 0 0 0 0 6 15 1 0 0 0 0 6 16 1 0 0 0 0 17 21 1 0 0 0 0 18 19 1 0 0 0 0 18 20 1 0 0 0 0 21 22 1 0 0 0 0 M END On 1/14/10 9:42 PM, Robert Hanson hans...@stolaf.edu wrote: On Thu, Jan 14, 2010 at 1:07 PM, Grossman, Robert B robert.gross...@uky.edu wrote: (1) Display H atoms. If I load a structure that does not show H atoms, it would be nice to have Jmol calculate their positions and display them. I know it must know that they are there, because when I loaded a structure with a planar C the the center of an isopropyl group, then minimized the structure, it converted the C to tetrahedral. (I guess it's possible you have this feature, but I'm not able to find it.) Jmol doesn't know they are there. The UFF calculation is simply optimizing the single-bond C-framework. If the problem can be better defined, we might be able to do something about it. Certainly would be a good trick. Do you have the bonding already -- double, triple? One problem, for example, is: C -C-O is that CH3CH2OH? CH2CH2OH? CH2C=O? CH3CHO? If the bonding is there, then we are ok; if it is not, then But if you have double bonds, it's easy. Send me a file. Bob -- 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
[Jmol-users] Jmol demo page hangs
Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- 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
[Jmol-users] jmolAppletInline and jmolLoadInline
Further diagnosis. Both jmolAppletInline() and jmolLoadInline() fail to display a molecule. I've successfully reproduced the problem on my own Web page, just trying to display a simple MOL file. I'm using Safari 4.0.4 on MacOS 10.5.8 and Jmol 11.8.15. From: Grossman, Robert B robert.gross...@uky.edu Reply-To: jmol-users@lists.sourceforge.net Date: Wed, 13 Jan 2010 13:12:08 -0500 To: jmol-users@lists.sourceforge.net Conversation: Jmol demo page hangs Subject: [Jmol-users] Jmol demo page hangs Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- 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
Re: [Jmol-users] Jmol demo page hangs
Thanks for your help, Otis. Unfortunately, your approach won't work for me; we acquire the data from a Java variable whose value in turn we acquire from a database. We use MOL files in Javascript variables with \n at the end of each line as input for other applets, e.g., MarvinSketch and MarvinView. So I think this is not a platform problem, but a Jmol problem. From: Otis Rothenberger o...@chemagic.com Reply-To: jmol-users@lists.sourceforge.net Date: Wed, 13 Jan 2010 13:47:56 -0500 To: jmol-users@lists.sourceforge.net Conversation: [Jmol-users] Jmol demo page hangs Subject: Re: [Jmol-users] Jmol demo page hangs Hello Bob, I see the same thing with Firefox and XP. I notice that the page source ends coordinate file lines with \n - linefeed. I wonder if this is a cr/lf issue. I run into this problem frequently. I'm not sure about a cross platform solution, but I wonder is ending the lines with \r\n would work on your system. Alternatively, I've had luck with loading an inline file from the JME applet into Jmol with the following direct approach: document.getElementById(MyAppleName).loadInlineString(jmeString, hover %a atomno=%i;echo;isosurface '';mo translucent;isosurface translucent;, false); Ignoring my load script, jmeString is simply the un-doctored coordinate string (molfile) from JME - i.e. no concatenated LF or CR/LF. Otis -- Otis Rothenberger http://chemagic.org On Wed, Jan 13, 2010 at 1:12 PM, Grossman, Robert B robert.gross...@uky.edu wrote: Hi, I'm trying to figure out how to load molecular structures into Jmol from JavaScript variables (instead of files). When I go to the demo page http://jmol.sourceforge.net/demo/jssample2/ , Jmol fails to load. That is, it says, Loading Jmol applet ... and the clock begins, but it never finishes loading. ??? -- Bob -- 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 -- 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
Re: [Jmol-users] Jmol demo page hangs
Thanks Angel. I've changed my invocation of Jmol as follows:
script type=text/javascript
jmolInitialize('%= pathToRoot %nosession/jmol');
jmolApplet([250, 250]);
jmolLoadInline('%= Utils.toValidJS(calcResults) %');
/script
It compiles at runtime as,
jmolInitialize('../../nosession/jmol');
jmolApplet([250, 250]);
jmolLoadInline('\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 -0.8168
0.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.10231.2313
0. O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53131.2313
0. 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
But although it now appears to load, I don't see a molecule in the viewer.
Furthermore, if I try to open another Jmol applet (with the first page open or
closed), Safari hangs.
From: Angel Herráez angel.herr...@uah.es
Reply-To: jmol-users@lists.sourceforge.net
Date: Wed, 13 Jan 2010 14:26:28 -0500
To: jmol-users@lists.sourceforge.net
Conversation: [Jmol-users] Jmol demo page hangs
Subject: Re: [Jmol-users] Jmol demo page hangs
Bob G., thanks for reporting this.
I've run a quick check with a local copy of the offending page, and it's not an
issue of
linefeeds.
It's a bug in Jmol. I can trace it back to between 11.8.7 and 11.8.11.
11.8.15 (the current version at the website) and 11.9.13 fail too.
jmolLoadInline() works fine even with 11.8.15.
It's just jmolAppletInline() that has the problem.
If you change it to
jmolAppletInline(200, )
then the radio buttons that call jmolLoadInline() work fine.
And I've done all that using the Jmol.js of 11.8.15, so it's not a Jmol.js bug
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Re: [Jmol-users] Jmol demo page hangs
Thanks, it displays now. 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
[Jmol-users] Jmol usually not displaying molecule
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 -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 -0.8168
0.81880. C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.1023
1.23130. O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.53131.2313
0. 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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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
