Re: [Jmol-users] Jmol SVG energy graph
Hi Jeff Report of my testing in WinXP (Firefox 3.0.7, Safari 4beta, Opera 9.63): Internet Explorer (v8) just refuses to open the xhtml page. In Opera everything works OK. > When you hover over a point on the graph it should be highlighted in yellow No yellow highlight in Firefox. In Safari, all points are at the top border of the SVG graph. Apart from that, they do work (yellow, red, model change) > and display the energy associated with that point in green Ok in Firefox. I can't see the label in Safari (may be above the top of the graph). > When you click on a point it should change to red and display the > corresponding model in the Jmol applet. Ok in Firefox and Safari. > When you select a model in the Jmol applet it should change the corresponding > point on the graph to red. The graph is not updated in Firefox. In Safari, similar to your report, I need to move the mouse pointer before the red point is updated (no need to click, it seems, just move it) HTH Great work! -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol SVG energy graph
I've made quite a bit of progress on using svg to graph data from a multiple model file in Jmol. Please take a look at http://web.me.com/jhansen4/iWeb/Jmol/svgGraphTest4.xhtml and let me know what you think. The page describes how it should behave and known problems. i would appreciate any help anyone could provide to take this further. *** Jeff Hansen Department of Chemistry and Biochemistry DePauw University 602 S. College Ave. Greencastle, IN 46135 jhan...@depauw.edu *** -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Java console error: falseAWT-EventQueue
that would be one of my debugging messages. Ignore that. 2009/6/1 Angel Herráez > Dear Jmol users, > > I am editing a page with 25 JmolApplets and I am gettign a bunch of Java > errors like this: > > applet test Jmol.java:update: paint falseAWT-EventQueue-6 > Thread[AWT-EventQueue- > 6,4,file:/R:/ABC/-threadGroup] > > Anyone can give me a clue as to what's going on? The applets display Ok but > I've never > had this error before. > > That's 11.6.23 unsigned > > Thanks > Angel > > > > -- > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > looking to deploy the next generation of Solaris that includes the latest > innovations from Sun and the OpenSource community. Download a copy and > enjoy capabilities such as Networking, Storage and Virtualization. > Go to: http://p.sf.net/sfu/opensolaris-get > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users > -- Robert M. Hanson Professor of Chemistry St. Olaf College 1520 St. Olaf Ave. Northfield, MN 55057 http://www.stolaf.edu/people/hansonr phone: 507-786-3107 If nature does not answer first what we want, it is better to take what answer we get. -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900 -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
On Tue, Jun 2, 2009 at 1:15 AM, Brian Salter-Duke wrote: > On quality, I think that is a different and general concern. We try to > not use poor quality images, so we would try to use only good quality > Jmol data files. I am happy that we restrict the type of jmol files to a > small number, perhaps initially only *.pdb files. Of course we would > have to add file extensions for jmol files to the upload process anyway, > so we would not need to add all possible file extensions. PDB is not a good format for small molecules; CML would be much better, e.g. by allowing embedding of important information regarding identification of the structure, or adding info on who added that image. Please be specific when you suggest file formats: there are two main areas of interest here: protein (PDB is the de facto standard), small molecules. In both cases, there are many alternative, and PDB as format has, at least, lesser quality than other offerings. I also really don't get the security concerns brought up... sorry, for dropping in on this, but have been involved in talk several years ago too, and if you want Jmol without JavaScript, that is no problem. JavaScript as security problem regarding a Jmol extension for WP is a non-issue. People have been using plain HTML for embedding Jmol in various website for more than 10 years, and I have no clue why this would not be a problem for WP. Please explain. Egon -- Post-doc @ Uppsala University http://chem-bla-ics.blogspot.com/ -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JMOL and Wikipedia
Brian wrote > On quality, I think that is a different and general concern. We try to > not use poor quality images, so we would try to use only good quality > Jmol data files. I am happy that we restrict the type of jmol files to a > small number, perhaps initially only *.pdb files. Of course we would > have to add file extensions for jmol files to the upload process anyway, > so we would not need to add all possible file extensions. I'm sorry if I was cryptic. By using Jmol, the WP already would exclude one source of lower quality images, per se. My hopes for advancement already went further, privately, and I took the chance to discuss here what should have been subject on other lists. However, I think your idea to restrict input to the PDB format, together with the demand to give either a ref to a paper, or full data to reproduce the positions (model type, impementation, parameters) would go a long way towards assuring the goal. Regards, ralf -- OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
