[Jmol-users] Jmol doen't read STO orbitals of molden file
Hello, My name is Nikiforov Alexander. I'm a PhD student at MPI for Coal Research in Muelheim an der Ruhr. I use Jmol in my research of conical intersections of small molecules. The problem is, Jmol cannot show me STO orbitals in molden file. Jmol reads orbitals and you can see how many orbitals in Script Console, but when you try to plot orbitals, it doesn't work. In Jmol Java Console it writes: MO ERROR: No basis functions found in file for MO calculation. (GAUSSIAN 'gfprint' keyword may be missing?) I tried to google the problem, but I don't think many people use STO orbitals today, still I perform OM2 semi-empirical calculations, so I have only STO orbitals. So, could you please help me to fix this. Attached is the example molden file that provides error. -- Regards, Nikiforov Alexander PhD student Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 45470 Mülheim an der Ruhr/Germany Tel.: +49 151 703-29-312 email: nikif...@mpi-muelheim.mpg.de http://webmail.mpi-muelheim.mpg.de/src/compose.php?send_to=nikiforo%40mpi-muelheim.mpg.de water.molden Description: Binary data -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol 14.0.0
Excellent - it works! Thanks very much Simon Quoting Robert Hanson hans...@stolaf.edu: please try http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.25c.zip Not only was there an issue with the applet, Jmol was not filtering the atoms correctly, either. These look MUCH better! On Mon, Nov 25, 2013 at 3:05 PM, s...@publcif.co.uk wrote: Good to see that the Java certification issue seems to be sorted. With respect to bug-fix requests, I'm still experiencing the following problem: calling: load =3fsx.cif filter ASSEMBLY 1 works in the Java application *only*. That is, it causes the Java Applet to 'hang' and produces the following error using JSmol: File Error:ERROR creating model: TypeError: biomolecules.get(...).get(...) is null script ERROR: ERROR creating model: TypeError: biomolecules.get(...).get(...) is null load =3fsx.cif filter ASSEMBLY 1 I'm seeing this whereever I try it (various machines, various web sites, and with various pdb mmcifs) so I suspect it is a genuine bug? Cheers Simon NB. load =3fsx.cif filter ASSEMBLY 2 works fine - its just the '1_555' assembly that hangs Quoting Robert Hanson hans...@stolaf.edu: Seems to me it's been over a year since we went Jmol 13, and in that time all the business of JSmol and Java issues and integration with JSpecView and JSME have come to pass. Time for a new major version number, I think. I would like to retire Jmol 13.3 and 13.2 and release Jmol 14.0 by the end of the week. Please send all bug fix requests as soon as possible directly to this list. Very latest, with fixes for mouse wheel binding, load monitor transparency, load() function security, local JNLP applet loading, new _use _jar and _j2s URL options, but not Safari local applet loading, can be found at http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.25.zip Bob -- 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Safari errors
I am looking at your web site the test2. Works fine in firefox. In safari both jsmol and jmol initially load fine. However, with the jsmol, after clicking number of links in the database column, the browser hangs and the page has to be reloaded. In addition, I get the following error alert popping up with a protein structure: Javascript JmolCore.js synchronus binary file transfer is requested but not available. Clicking OK on this alert allows that structure and a few others to load, but then it again freezes. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Addendum
I do not have the aforementioned issue running from my desktop using ….25c. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Safari errors
Phil, What version of Safari are you using? For me, Safari iPad and Safari Desktop became complete busts after an update to Mavericks and the Mavericks' Safari - hangs and crashes. For the most part, my problems are only with scripting. JSmol itself seems OK. Scripts are completely unpredictable. I'm not even sure I see a pattern. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org From: Philip Bays pb...@saintmarys.edu Sent: Tuesday, November 26, 2013 8:30 AM To: Jmol Jmol jmol-users@lists.sourceforge.net Subject: [Jmol-users] Safari errors I am looking at your web site the test2. Works fine in firefox. In safari both jsmol and jmol initially load fine. However, with the jsmol, after clicking number of links in the database column, the browser hangs and the page has to be reloaded. In addition, I get the following error alert popping up with a protein structure: Javascript JmolCore.js synchronus binary file transfer is requested but not available. Clicking OK on this alert allows that structure and a few others to load, but then it again freezes. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Safari errors
Mavericks and Safari 7. I am off to grandparents day this morning at our granddaughter's grade school. I will get back to this afternoon. J. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 Sent from my iPhone On Nov 26, 2013, at 8:37 AM, Otis Rothenberger osrot...@chemagic.com wrote: Phil, What version of Safari are you using? For me, Safari iPad and Safari Desktop became complete busts after an update to Mavericks and the Mavericks' Safari - hangs and crashes. For the most part, my problems are only with scripting. JSmol itself seems OK. Scripts are completely unpredictable. I'm not even sure I see a pattern. Otis -- Otis Rothenberger Department of Chemistry Illinois State University Normal, IL 61790-4160 http://chemagic.org -- *From*: Philip Bays pb...@saintmarys.edu *Sent*: Tuesday, November 26, 2013 8:30 AM *To*: Jmol Jmol jmol-users@lists.sourceforge.net *Subject*: [Jmol-users] Safari errors I am looking at your web site the test2. Works fine in firefox. In safari both jsmol and jmol initially load fine. However, with the jsmol, after clicking number of links in the database column, the browser hangs and the page has to be reloaded. In addition, I get the following error alert popping up with a protein structure: Javascript JmolCore.js synchronus binary file transfer is requested but not available. Clicking OK on this alert allows that structure and a few others to load, but then it again freezes. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Safari
So I am testing this on my office 2.7 GHz i5 8 GB 1600 MHz DDR3 Mac, and I am just totally blown away. I just saw the local signed Java applet load a PDB file and 2.2MB electron density map in the amount of time it took to release my mouse. HOLY COW! (JavaScript version did that in 2 seconds.) Bob On Tue, Nov 26, 2013 at 2:32 PM, Robert Hanson hans...@stolaf.edu wrote: Please try http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.26.zip I think I broke some aspects of the tests in that last upload.. Also, this version does away with the multitude of language jar files, adding a directory jsmol/idioma instead. Bob On Tue, Nov 26, 2013 at 1:08 PM, Philip Bays pb...@saintmarys.edu wrote: Otis raised a question about Safari earlier this morning (unfortunately, I accidentally deleted it.) I find that Bob’s page (test2) which uses yesterdays release c is not working for me on either my Mac or a brand new iPad (my son’s). Both are running the latest version of Safari. Furthermore, it is not now running on Firefox. The first three lines of the initial (HTML5) applet load are visible in the applet window, but then it hangs. This is the case in FF and Safari on all Apple platforms at my disposal. However, that same version loads fine locally, including both signed and unsigned java applets. I still see the freezes after multiple structure loads that I comments on this morning. Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list 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 -- 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-JSO - custom pre-/post-processing script
Am 26.11.2013 21:28, schrieb Robert Hanson: JSmol does not ignore the refresh, but remember there is only one thread, so if your timeouts on the fade don't get processed before the moveto continues, you may see no message. (Guessing here) Obviously I wasn't clear enough. It is the other way round. With a command like 'moveto', with a built-in refresh, the wait message is visible. With other commands it is not, although I havn't tested this very extensively. It was just the most obvious difference between the scripts with and without a visible wait message. And the behaviour is the same in Jmol if the explicit 'refresh' command is removed. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
Yes, it's related to the fact that BondSet is an inner class of Bond. Something is as happening out of order. Utlimately, Bond.BondSet is created just fine. Very curious! On Tue, Nov 26, 2013 at 12:02 AM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: The “Bond/BondSet.js” error appears also on Mac Firefox 25.0.1, but the applet continues working. You may see error reports with Firebug. This might come from lines like this one in Bond.js and other files: J/modelset/Bond.js:Clazz.superConstructor (this, J.modelset.Bond.BondSet, []); The call to superConstructor assumes that J, modelset and Bond are directories, while BondSet is a file with the ‘.js’ extension. Jaim On Nov 26, 2013, at 12:02 AM, Robert Hanson hans...@stolaf.edu wrote: The Bond/BondSet.js message is certainly curious, but it's not a show stopper. This appears even on web-site access via Safari. The message just after that is the killer, having to do with not being able to load core.z.js. Safari (like Chrome or Firefox without special settings) will not allow access to local files. The yellow box should be gone now for Safari hosted access to Jmol. The problem was that apparently Safari is no longer accepting the object tag. The applet tag is required so that you can click on the windows and accept the website for the applet. Must be a bug, but I have switched JSmol to the applet tag when it detects Safari. There is still a problem with local file reading. It looks to me as though Safari is not recognizing local JNLP applications within the browser. Or there is some setting we are missing. Firefox is working fine for Safari local file access, so I concur with Phil and suggest we just write off Safari for now. Bob On Mon, Nov 25, 2013 at 9:09 AM, Philip Bays pb...@saintmarys.edu wrote: I meant this version of Safari, not this version of Jmol!! Safari has lots of quirks right now, I think. I still am not able to run jmol locally, because I get a Safari message that java is not enables, despite the fact that I have it enabled anyplace I can find to enable it. But firefox works fine so that is what I will use for the time being. On Nov 25, 2013, at 10:04 AM, Robert Hanson hans...@stolaf.edu wrote: Anything you can send me would be helpful. I will test Safari locally here today and see what I can find. On Mon, Nov 25, 2013 at 4:12 AM, Philip Bays pb...@saintmarys.eduwrote: Oh, yes. I see them scroll by as the applet is loading and can see them using the SHOW link. So we will just attribute this to a Safari flaw — like a lot of others in this version!! On Nov 24, 2013, at 5:29 PM, Robert Hanson hans...@stolaf.edu wrote: There should be a whole flood of messages in Jmol's Java console. (Behind the applet and visible with the Info SHOW link under the applet.) No? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk ___ Jmol-users mailing list 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 -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now. http://pubads.g.doubleclick.net/gampad/clk?id=63431311iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Shape the Mobile Experience: Free Subscription Software experts and developers: Be at the forefront of tech innovation. Intel(R) Software Adrenaline delivers strategic insight and game-changing conversations that shape the rapidly evolving mobile landscape. Sign up now.
[Jmol-users] Firefox/Mac loads Signed local Jmol but not Unsigned
On Tue, Nov 26, 2013 at 2:32 PM, Robert Hanson hans...@stolaf.eduhttp://stolaf.edu wrote: Please try http://chemapps.stolaf.edu/jmol/zip/jmol-13.3.9_2013.11.26.zip With this version and test2.htm Firefox loads the signed Jmol just fine but Unsigned gives an AccessControlException error. Is this expected? Safari also loads the signed Jmol fine but not unsigned. It also stalls when loading JSmol. Others have noted the Bondset.js problem. loading... j2s/J/util/ModulationSet.js loading... j2s/J/modelset/Bond/BondSet.js -- required by w3c script failed Jmol JavaScript applet jmolApplet0_object__788223534822464__ initializing getValue debug = null getValue logLevel = null getValue allowjavascript = true AppletRegistry.checkIn(jmolApplet0_object__788223534822464__) In contrast Firefox is fine with JSmol. Best regards Nick -- Nick Greevesvia OS X Mail Director of Teaching and Learning Department of Chemistry University of Liverpool Donnan and Robert Robinson Laboratories Crown Street, LIVERPOOL L69 7ZD U.K. Email address:ngree...@liverpool.ac.ukmailto:ngree...@liverpool.ac.uk WWW Pages:http://www.chemtube3d.com Tel:+44 (0)151-794-3506 (3500 secretary) Dept Fax: +44 (0)151-794-3588 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-JSO - custom pre-/post-processing script
try adding a delay of a fraction of a second. I think your script is just too fast. What about slower scripts, like isosurface creation? Just to be clear, JSmol and Jmol are really one thing; both Java and HTML5, so let's call these with Java and with HTML5 or something like that rather than JSmol and Jmol. Bob On Tue, Nov 26, 2013 at 3:49 PM, Rolf Huehne rhue...@fli-leibniz.de wrote: Am 26.11.2013 22:15, schrieb Robert Hanson: I misunderstood. Somehow thought we were talking about the monitor message still. All my tests with set echo top left;echo xxx;refresh;more here..;echo; work fine. Can you give me some example that does not? There might be some platfom-specific differences. With Firefox 25.0 on Win7 on my laptop at home the wait message seems to be always wisible. With Firefox 25.0 on Linux at the office it wasn't. I will try it again tomorrow. An example command would be background black (size: 600x600 pixel). With Jmol on Linux the wait message was most of the time visible for a small fraction of a second, but never with JSmol. On Win7 it is now always visible in JSmol (and much longer than in Jmol on Linux). Interestingly and somehow in contrast to the above, the JSmol speed increased on my laptop by a factor of about 10 (regarding the number of atoms, roughly comparing the rotation speed with about 5000 and 5 atoms) after I updated a few days ago from Firefox version 22 to 25. The Firefox update was the only change. But with Firefox version 25 on Linux the speed is about the same as with Firefox 22 on Win7. Regards, Rolf -- Rolf Huehne Postdoc Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI) Beutenbergstrasse 11 07745 Jena, Germany Phone: +49 3641 65 6205 Fax: +49 3641 65 6210 E-Mail: rhue...@fli-leibniz.de Website: http://www.fli-leibniz.de Scientific Director: Prof. Dr. K. Lenhard Rudolph Head of Administration: Dr. Daniele Barthel Chairman of Board of Trustees: Dennys Klein VAT No: DE 153 925 464 Register of Associations: No. 296, Amtsgericht Jena Tax Number: 162/141/08228 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list 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 -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol-JSO - custom pre-/post-processing script
Rolf, I just found a bug in the GUI for JSmol that made it so that MSIE
executed commands in the search box twice -- I think it may be the same
with JenaLib:
input class=jmol type='text' id='jmol_command' size='30'
onKeypress='if (event.keyCode == 13) {idbSubmitScript()}'
input class=jmol id=run_jmol_command type=button
onClick='idbSubmitScript()' value=run
At least for me, a combination just like that on jsmol.htm fired both
onKeyPress and onClick -- same command twice -- in MSIE specifically. So
all my hand-entered commands were being executed twice!
At least for me, I had to change that onKeyPress to:
onKeypress='if (event.keyCode == 13) {idbSubmitScript(); return false}
Nasty!
Also, this next part probably doesn't have anything to do with your
business, but I thought I would let you know anyway. To complicate things,
my threading interrupts made the two issuances occur concurrently and
produced very strange results. Particularly when I issued this command:
!set echo top left; t=now();refresh;isosurface vdw;t = now(t);echo @t
If this command is given twice, rapidly, then the echo is not what you
might expect:
41
391189626
Whoah! Setting debugScript TRUE, we see what is happening:
$ !t = now(); delay 5;t = now(t);echo @t
t = now();
delay 5;
$ !t = now(); delay 5;t = now(t);echo @t
t = now();
delay 5;
t = now(t); // return from the FIRST delay
echo @t;
41
t = now(t); // return from the SECOND delay!
echo @t;
391189626
That's because of the !, which interrupts the first script and starts the
second. And the fact that I am repurposing the variable t. Here it is
without the !:
$ t = now(); delay 5;t = now(t);echo @t
t = now();
delay 5;
$ t = now(); delay 5;t = now(t);echo @t
t = now(t);
echo @t;
5027
t = now();
delay 5;
t = now(t);
echo @t;
5049
My mistake to leave that ! in there
Bob
On Tue, Nov 26, 2013 at 6:29 PM, Robert Hanson hans...@stolaf.edu wrote:
try adding a delay of a fraction of a second. I think your script is just
too fast. What about slower scripts, like isosurface creation?
Just to be clear, JSmol and Jmol are really one thing; both Java and
HTML5, so let's call these with Java and with HTML5 or something like
that rather than JSmol and Jmol.
Bob
On Tue, Nov 26, 2013 at 3:49 PM, Rolf Huehne rhue...@fli-leibniz.dewrote:
Am 26.11.2013 22:15, schrieb Robert Hanson:
I misunderstood. Somehow thought we were talking about the monitor
message still. All my tests with
set echo top left;echo xxx;refresh;more here..;echo;
work fine. Can you give me some example that does not?
There might be some platfom-specific differences. With Firefox 25.0 on
Win7 on my laptop at home the wait message seems to be always wisible.
With Firefox 25.0 on Linux at the office it wasn't. I will try it again
tomorrow.
An example command would be background black (size: 600x600 pixel).
With Jmol on Linux the wait message was most of the time visible for a
small fraction of a second, but never with JSmol. On Win7 it is now
always visible in JSmol (and much longer than in Jmol on Linux).
Interestingly and somehow in contrast to the above, the JSmol speed
increased on my laptop by a factor of about 10 (regarding the number of
atoms, roughly comparing the rotation speed with about 5000 and 5
atoms) after I updated a few days ago from Firefox version 22 to 25. The
Firefox update was the only change. But with Firefox version 25 on Linux
the speed is about the same as with Firefox 22 on Win7.
Regards,
Rolf
--
Rolf Huehne
Postdoc
Leibniz Institute for Age Research - Fritz Lipmann Institute (FLI)
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Phone: +49 3641 65 6205
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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 Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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Re: [Jmol-users] Firefox/Mac loads Signed local Jmol but not Unsigned
I agree with Nick on this for the most part. However, for me Firefox hangs after several loads from the database column; the culprit seems to be caffeine with MMFF force field. On Nov 26, 2013, at 5:48 PM, Greeves, Nick ngree...@liverpool.ac.uk wrote: With this version and test2.htm Firefox loads the signed Jmol just fine but Unsigned gives an AccessControlException error. Is this expected? Philip Bays Emeritus Professor of Chemistry Saint Mary's College Notre Dame, IN 46556 pb...@saintmarys.edu -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Please test (2)
On Nov 27, 2013, at 12:30 AM, Robert Hanson hans...@stolaf.edu wrote: Yes, it's related to the fact that BondSet is an inner class of Bond. Something is as happening out of order. Utlimately, Bond.BondSet is created just fine. Very curious! Found in your code a few other calls to Clazz.superConstructor( that would generate a non-existing file path, like it happens with J.modelset.Bond.BondSet Are these working Ok? If this is the case, then why? J.jvxl.calc.MarchingSquares.ContourVertex J.jvxl.readers.Dsn6BinaryReader JSV.source.JSVXmlReader.DataBuffer JZ.Inflate.Return Jaim -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get 100% visibility into your Java,.NET, PHP application. Start your 15-day FREE TRIAL of AppDynamics Pro! http://pubads.g.doubleclick.net/gampad/clk?id=84349351iu=/4140/ostg.clktrk ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
