From wdecatur at yahoo.com Thu Jan 16 12:55:26 2014 From: wdecatur at yahoo.com (Wayne Decatur) Date: Thu, 16 Jan 2014 09:55:26 -0800 (PST) Subject: [Proteopedia] Keeping Proteopedia scenes working Message-ID: <1389894926.81927.YahooMailNeo@web120702.mail.ne1.yahoo.com> Some of you may notice you are having a problem seeing 3D, interactive structures in Proteopedia today. A large change in how Java is enabled has taken effect. In the short term you will need to add Proteopedia to a trusted exceptions list for Java on your own computer. We have described how to do that at http://proteopedia.org/wiki/index.php/Java#Adding_Proteopedia_to_the_Java_Exceptions_list . Jaim is working hard on updating it so that Protepedia will use the new version of Jmol that does not trigger these security concerns. Jaim is working hard on making it so that Proteopedia can very soon also work without Java. This allows mobile devices like the iPad and Android devices to view and author all aspects of Proteoepdia. Even 3D structure scenes. This will be a significant move forward and requires Herculean efforts of development. It is coming very soon though. Thanks, Wayne Editorial Board of Proteopedia -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Sun Jan 26 03:47:40 2014 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Sun, 26 Jan 2014 08:47:40 +0000 Subject: [Proteopedia] running on HTML5, optional Java Message-ID: Starting now, Sunday Jan 26 2014 early morning, Proteopedia uses by default HTML5 instead of Java for rendering interactive models. We run on the latest stable version of Jmol 14.0.7 Huge thanks to Wayne Decatur for SAT (Scene Authoring Tool) testing on iPad and desktop, to Alexander Berchansky for testing also on IExplorer and Bob Hanson and the Jmol Team. Please report to jaime.prilusky at weizmann.ac.il any problem you may encounter. Positive issues: Page, scene rendering and editing works on most browsers and platforms, including iPad. Negative aspects: Large structures will take longer to load, render and rotate. You may request Java on a single page by adding ?_USE=JAVA to the URL, as in: http://proteopedia.org/w/1pdb?_USE=JAVA If you still want to use Java by default: Login Proteopedia.org, go to http://proteopedia.org/w/Special:Preferences , click on the Misc tab, check the box ?Use Java for rendering structures? and Save. Known problems: Additional applets besides the first one, on multi-applet pages, might not work on HTML5. Working on fixing. Better option, try converting your page to the single applet scrolling page layout: is memory efficient and user friendly. Jaim __ Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: Jaime.Prilusky at weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ -------------- next part -------------- An HTML attachment was scrubbed... URL: From jaime.prilusky at weizmann.ac.il Tue Mar 25 03:49:53 2014 From: jaime.prilusky at weizmann.ac.il (Jaime Prilusky) Date: Tue, 25 Mar 2014 07:49:53 +0000 Subject: [Proteopedia] Jmol upgrade 14.1.12 Message-ID: Proteopedia is running now on the very latest version of Jmol 14.1.12 If you encounter any problems, please try restarting/clearing cache of your browser to ensure that all pieces of the new software got loaded. Regards, Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: Jaime.Prilusky at weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ From wdecatur at yahoo.com Thu Mar 27 09:27:38 2014 From: wdecatur at yahoo.com (Wayne Decatur) Date: Thu, 27 Mar 2014 06:27:38 -0700 (PDT) Subject: [Proteopedia] Jmol upgrade 14.1.12 In-Reply-To: References: Message-ID: <1395926858.42872.YahooMailNeo@web120704.mail.ne1.yahoo.com> Sorry, Jaim. Just fished this out of my spam. I am planning to try making some scenes in the next few days and so I'll let you know if I see anything odd. ________________________________ From: Jaime Prilusky To: "proteopedialist-for-users at bioinformatics.org" Sent: Tuesday, March 25, 2014 3:49 AM Subject: [Proteopedia] Jmol upgrade 14.1.12 Proteopedia is running now on the very latest version of Jmol 14.1.12 If you encounter any problems, please try restarting/clearing cache of your browser to ensure that all pieces of the new software got loaded. Regards, Jaim -- Dr Jaime Prilusky Head Bioinformatics R&D Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel mail: Jaime.Prilusky at weizmann.ac.il tel: 972-8-9344959 fax: 972-8-9344113 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) ------------------------------------------------------------------------ _______________________________________________ Proteopedialist-for-users mailing list Proteopedialist-for-users at bioinformatics.org http://www.bioinformatics.org/mailman/listinfo/proteopedialist-for-users -------------- next part -------------- An HTML attachment was scrubbed... URL: