## jmol-developers — Detailed discussions about the source code by and for Jmol developers

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 Re: [Jmol-developers] bug in Java applet? JSmol 13.2.4 and 13.3.4 From: Angel Herráez - 2013-09-16 09:15:51 Thanks, Bob Version from your site is working fine, thanks. I've corrected the link in Jmol Wiki I vote for removing the corrupt and buggy version(s) from SourceForge if possible. Users will become confused if a download does not behave. 
 Re: [Jmol-developers] bug in Java applet? JSmol 13.2.4 and 13.3.4 From: Robert Hanson - 2013-09-14 18:28:38 Attachments: Message as HTML (and that has just been updated to allow for local file reading. See top center link at http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm I'm hoping that works for Macs. Tested using Chrome, FireFox, and MSIE10. This should go a long way toward replacing the signed applet. Suggestions welcome. On Fri, Sep 13, 2013 at 2:10 PM, Rolf Huehne wrote: > Am 13.09.2013 18:06, schrieb Angel Herráez: > > Dear Bob, > > > > I need a working version of JSmol with HTML and alternative Java. > > I am having problems to get one: > > > > * jsmol-13.2.4.zip from JSmol site at SF has a bug in the Java mode > > (tested with the simple.htm included in that zipfile, switched to > > signed applet) : the mouse does not XY-rotate, but instead Z-rotates > > or zooms > > > > * jsmol-13.3.4.zip, same problem > > > > * jsmol-13.3.5.zip from JSmol site at SF is corrupt > > > > * I can see no jsmol.zip file at StOlaf > > > > Any hints? > > > At the top of the JSmol page > http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm > > there is a link to a ZIP file from 2013/09/09: > http://chemapps.stolaf.edu/jmol/zip/Jmol.zip > > The ZIP file also contains a 'jsmol.zip' file from the same date. > > 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: rhuehne@... > 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 > > > > ------------------------------------------------------------------------------ > How ServiceNow helps IT people transform IT departments: > 1. Consolidate legacy IT systems to a single system of record for IT > 2. Standardize and globalize service processes across IT > 3. Implement zero-touch automation to replace manual, redundant tasks > http://pubads.g.doubleclick.net/gampad/clk?id=51271111&iu=/4140/ostg.clktrk > _______________________________________________ > Jmol-developers mailing list > Jmol-developers@... > https://lists.sourceforge.net/lists/listinfo/jmol-developers > -- 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 
 Re: [Jmol-developers] bug in Java applet? JSmol 13.2.4 and 13.3.4 From: Rolf Huehne - 2013-09-13 19:11:02 Am 13.09.2013 18:06, schrieb Angel Herráez: > Dear Bob, > > I need a working version of JSmol with HTML and alternative Java. > I am having problems to get one: > > * jsmol-13.2.4.zip from JSmol site at SF has a bug in the Java mode > (tested with the simple.htm included in that zipfile, switched to > signed applet) : the mouse does not XY-rotate, but instead Z-rotates > or zooms > > * jsmol-13.3.4.zip, same problem > > * jsmol-13.3.5.zip from JSmol site at SF is corrupt > > * I can see no jsmol.zip file at StOlaf > > Any hints? > At the top of the JSmol page http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm there is a link to a ZIP file from 2013/09/09: http://chemapps.stolaf.edu/jmol/zip/Jmol.zip The ZIP file also contains a 'jsmol.zip' file from the same date. 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: rhuehne@... 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 
 [Jmol-developers] bug in Java applet? JSmol 13.2.4 and 13.3.4 From: Angel Herráez - 2013-09-13 16:07:14 Dear Bob, I need a working version of JSmol with HTML and alternative Java. I am having problems to get one: * jsmol-13.2.4.zip from JSmol site at SF has a bug in the Java mode (tested with the simple.htm included in that zipfile, switched to signed applet) : the mouse does not XY-rotate, but instead Z-rotates or zooms * jsmol-13.3.4.zip, same problem * jsmol-13.3.5.zip from JSmol site at SF is corrupt * I can see no jsmol.zip file at StOlaf Any hints? 
 Re: [Jmol-developers] Scripting Documentation - SVN and CSS From: Rolf Huehne - 2013-09-02 10:20:29 On 09/01/2013 11:47 AM, Rolf Huehne wrote: > Besides this I would propose some tweaks for the CSS of the > documentation. I have only checked them yet in Firefox 22.0 on Windows. > The attached picture shows how the tables are supposed to look with the > tweaks. > There were also some unexpected places with tables like 'examples'. But > I think they profit from the changes as well. > The tweaks are installed now at the Jena3D mirror (http://jena3d.fli-leibniz.de/doc/jmol_scripting.html) for testing until the next mirror update tomorrow morning (4 a.m. UTC). I tested now also in different browsers on Linux (Chromium 30.0, Firefox 22.0, Konqueror 4.8.5, Opera 12.16) and it looks identical and as expected. I also tested Internet Explorer 8.0 on WinXP which doesn't support the CSS3 "nth-child" option. I think it still looks ok. For me there are only two tables that would need an ID or something else to be able to apply individual styles: the graphics table in the "contact" section and the "General Parameters" table. 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: rhuehne@... 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. 230296, Amtsgericht Jena Tax Number: 162/141/08228 
 Re: [Jmol-developers] JSmol and java.lang.Error From: Geoffrey Rowland - 2013-09-01 10:55:21 Attachments: Message as HTML > [you must be working with Gareth, right?] No, I noticed the MathJax issue a while back. Gareth's post just prompted me to add a follow up. >So what is MathJax, and what does it have to do with Jmol? Sounds interesting.... Bob, I guess you now know what MathJax is. For anyone else, who is not familiar, MathJax is an open source JavaScript display engine for Mathematics (MathML and TeX) that works cross-browser http://www.mathjax.org/ So, for science-focused web content, CMSs, blogs, forums etc there may well be occasions when it would be nice to have MathML and and Jmol on the same page. I came across DragMath/MathJax in the context of Moodle and Mahara. https://moodle.org/mod/forum/discuss.php?d=201737 https://mahara.org/interaction/forum/topic.php?id=3759 BTW If anyone is looking for another Java-to-JavaScript conversion project ;-) DragMath is an open-source Java applet Equation Editor that works nicely with MathJax. http://www.dragmath.bham.ac.uk/ I'm aware of some other JavaScript Equation Editors such as WIRIS and CodeCogs, but they are all proprietary. http://www.wiris.com/ http://www.codecogs.com/latex/about.php > It's a pretty simple solution. Really what the problem is is that both > .Jmol and MathJax are competing for the AJAX processing. [snip] Thanks, Bob that was really useful. Ended up using a variation on your suggestion, to display JSmol after MathJax, similar to the following: MathJax.Hub.Queue(function () { loadJmol(); }); loadJmol = function() { Jmol.setDocument(0); Info.deferApplet = false; Info.deferUncover = true; jmol1 = Jmol.getApplet("jmol1", Info) $("#appletplace1").html(Jmol.getAppletHtml(jmol1)); Info.deferApplet = true; Info.deferUncover = true; jmol2 = Jmol.getApplet("jmol2", Info)$("#appletplace2").html(Jmol.getAppletHtml(jmol2)); } Finally, I have recently noticed that Opera (latest version 12.16 on Windows 7 or Fedora 19) is no longer displaying JSmol for binary files (e.g. .pse, .pdb.zip) on, say, http://chemapps.stolaf.edu/jmol/jsmol/jsmol.htm This was all working with Opera a few weeks ago though I'm not sure if recent Opera or JSmol updates have broken things. Perhaps related to the recent removal of 'JSmol hacks to jQuery'' which otherwise seems to work well. Cheers Geoff 
 [Jmol-developers] Scripting Documentation - SVN and CSS From: Rolf Huehne - 2013-09-01 09:48:31 Attachments: jmol_scripting_doc-example.jpg  Hi Bob and others, the scripting documentation in the SVN hasn't been updated for quite a while. This leads to a very outdated Jena3D mirror (http://jena3d.fli-leibniz.de/doc/jmol_scripting.html). The latest Jmol version for which documentation is available there is 12.4. I havn't complained yet because we are still using version 11.6 within Jena3D and the documentation for it vanished on the primary site. But since our version is supposed to be a mirror it shouldn't get too distant. But I would prefer that the documentation for 11.6 would be included again. Besides this I would propose some tweaks for the CSS of the documentation. I have only checked them yet in Firefox 22.0 on Windows. The attached picture shows how the tables are supposed to look with the tweaks. There were also some unexpected places with tables like 'examples'. But I think they profit from the changes as well. ====== CSS tweaks ============ table { border-spacing: 0px; border-collapse: collapse; border: 0px solid rgb(0,0,0); margin-left: 0.2em; margin-top : 0.2em; } td td { border-collapse: collapse; border: 0px solid rgb(42,182,255); padding-top: 0.2em; padding-bottom: 0.2em; padding-left: 0.4em; } td td { background-color: rgb(249,249,249); } td tr:nth-child(2n+1) > td { background-color: rgb(229,229,229); } td tr:nth-child(2n+1) > td:first-child { background-color: rgb(170,210,255); } td tr:nth-child(2n) > td:first-child { background-color: rgb(209,239,255); } td td td { background-color: rgb(219,219,219); } td td tr:nth-child(2n+1) > td { background-color: rgb(239,239,239); } td td tr:nth-child(2n+1) > td:first-child { background-color: rgb(143,224,191); } td td tr:nth-child(2n) > td:first-child { background-color: rgb(154,254,213); } ========================================= 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: rhuehne@... 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 
 [Jmol-developers] code revision of user interface for the JSmol pop-up menu From: Angel Herráez - 2013-09-01 09:30:24 Dear Bob, I've worked on some retouching of the user interface of the JSmol pop-up menu. I couldn't find what is the source file that produces this menu, so I downloaded the production file, http://chemapps.stolaf.edu/jmol/jsmol/j2s/core/coremenu.z.js dated 19-Aug-2013_17:25 and worked from that I am attaching - the original file (unpacked in some online beautifier´) - my modified file (unpacked) - a Unix diff file between them, for guidance ** The attachment goes in a separate private message, since it was rejected by SF ** I have tested in localhost and everything seems to behave well. A demo is available at http://biomodel.uah.es/Jmol/pop-up_menu/test_popupmenu.htm (see version 3) My motivations: - make the CSS rules isolated, i.e. applied only to jmolPopupMenu and not to other jQuery.menu instances that might be in the page - make it more compact (less tall, much less wide) - avoid the separators being visually active elements (on hover) - apply greyed-out style to disabled elements (rather than translucency), and make them visually inactive to mouse hover - avoid the # change in the url (by removing the href; this also seems to make the checkboxes more responsive) (Note) - added a ">" sign to expandable menu items - removed some css code that is not used by jmolPopupMenu - a more standard layout of html label tags, ie not surrounding the input tag The CSS is rather simplified, which should make easier for page developers to override some rules if they need (e.g. for finger-based devices). Still, there's quite a deal of mystery in some rules inherited from jQueryUI. I cleared up all that looked safe. Hope you can incorporate the changes. I think it feels quite better. --Note--: I tried to replace the a tags by span with a specific class (after all, they are not hyperlinks nor anchors), but it does not work. Seems that other code in the js file (coming from JQuery UI menu I believe) relies on them being 'a' tags, and I'd rather not mess up with that code. A flat seems to be fine, even if not semantically pure. `

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