[Jmol-users] Jmol extension for Mediawiki
Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it - Opening Jmol in a new window, that would be scalable - Disabling javascript in Jmol script - ... - anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] callback functions in JSmol
Dear JSmol users, I am trying to convert my Jmol page to JSmol but I have a problem with the callback functions. I was using jmolSetCallback( animFrameCallback , modelSelected); and converting that to jmolSetCallback(myJmol, animframecallback , modelSelected); did not work. I am sure there is an easy solution, I just did not find it anywhere. Thanks a lot for your help Christian - Dr. Christian Baerlocher Lab. of Crystallography ETH Zürich Wolfgang-Pauli-Strasse 10 CH-8093 Zürich -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] JSmol in XHTML
HI I've been trying to get JSmol to work with XHTML, and while the Java side works, the HTML5 does not. The cause of the problem is a TypeError: f is undefined in JSmol.min.js, line 393. With the culprit being f.appendChild(c) While trying to find the problem, I've noticed that, while the simple2.htm claims to be XHTML (and may validate as such), it does not work when served correctly to the browsers; IE, Firefox and Chrome all fail when the HTTP response identifies the Content-Type as application/xhtml+xml, which is required for correct processing of XHTML. After clearing most of the code for the leftpanel (undefined entities), rightpanel (not well formed) and lower panel (not well formed, mismatched tag), the page loads, adding ?USE=HTML5 results in the TypeError. Is there any likelihood of full XHTML support? TIA Kevin -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] callback functions in JSmol
Hello Christian I do not think there is a jmolSetCallback() in JSmol Try to use parameters in the Info variable http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Callbacks winmail.dat-- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
What I've learned... On Tue, Apr 23, 2013 at 10:13 AM, Nicolas Vervelle nverve...@gmail.comwrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities Doesn't work from a page-side perspective. You can't detect if Java is available any more, and when it is, the page holds until it is functional. So that's a real problem. From the server, you can certainly find out if it is mobile or not, and guess that only HTML5 will work. WebGL development is still minimal -- doesn't seem to be a future in that for the iPad; only minimally supported in JSmol. There's an image only option that I thought might allow the server to create the view and send it, but that turns out to require too much dead time waiting for the server to process the script. The only clear autoswitching that works from the page is If no HTML5, use Java for older browsers. - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it That's all set. It's a couple of flags in the Info block. This does work well. - Opening Jmol in a new window, that would be scalable All set, but not built in. I know someone was doing this. - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? - ... - anything you can think of Basically JSmol is precisely the same as Jmol, just all in JavaScript. Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] callback functions in JSmol
you can do it with a Jmol script, just as before: set animFrameCallback myCallback or, as Angel mentions, you can set it up in the Info array. On Tue, Apr 23, 2013 at 12:42 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: Hello Christian I do not think there is a jmolSetCallback() in JSmol Try to use parameters in the Info variable http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Callbacks -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol in XHTML
I'm not surprised. If you can help us do that, it would be great. You are using Jmol.setXHTML(id) ? I don't remember exactly how to test a page in XHTML, so if you would let me know, I can help you. Bob On Tue, Apr 23, 2013 at 11:07 AM, Kevin Milburn kmilb...@gpslsolutions.comwrote: HI ** ** I've been trying to get JSmol to work with XHTML, and while the Java side works, the HTML5 does not. ** ** The cause of the problem is a TypeError: f is undefined in JSmol.min.js, line 393. With the culprit being f.appendChild(c) ** ** While trying to find the problem, I've noticed that, while the simple2.htm claims to be XHTML (and may validate as such), it does not work when served correctly to the browsers; IE, Firefox and Chrome all fail when the HTTP response identifies the Content-Type as application/xhtml+xml, which is required for correct processing of XHTML. After clearing most of the code for the leftpanel (undefined entities), rightpanel (not well formed) and lower panel (not well formed, mismatched tag), the page loads, adding ?USE=HTML5 results in the TypeError. ** ** Is there any likelihood of full XHTML support? ** ** TIA Kevin -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] callback functions in JSmol
Many thanks for your quick help. I will try this tomorrow Christian On 23. Apr, 2013, at 8:29 PM, Robert Hanson hans...@stolaf.edu wrote: you can do it with a Jmol script, just as before: set animFrameCallback myCallback or, as Angel mentions, you can set it up in the Info array. On Tue, Apr 23, 2013 at 12:42 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: Hello Christian I do not think there is a jmolSetCallback() in JSmol Try to use parameters in the Info variable http://wiki.jmol.org/index.php/Jmol_JavaScript_Object/Info#Callbacks -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ 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 Chair, Chemistry Department 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 -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
- Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... winmail.dat-- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] JSmol in XHTML
One of the issues might be that, even if the page source code validates, the actual generated xhtml will not be compliant. ? winmail.dat-- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
On Tue, Apr 23, 2013 at 9:39 PM, Herráez Sánchez Ángel angel.herr...@uah.es wrote: - Disabling javascript in Jmol script Well, if it's all JavaScript, what does that mean? Time ago, one of the objections to include Jmol in Wikipedia was that arbitrary Javascript should not be allowed to execute from within a malicious Jmol Script. A flag was implemented to block javascript calls within Jmol scripts (and it is enabled by default, or may be enforced, in the Jmol MediaWiki Extension). Yes, it sounds funny now, but still there may be a basis for it. Don't know... Yes, that's what I meant by disabling javascript in Jmol script. I think it would still be an objection to include Jmol in a wiki if arbitrary Javascript could be executed through Jmol script. Since every user would be able to create the Jmol script, it should be safe for others to view it. Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Hi Jaime, Good to hear that you have kept working on this That would be great to have this packaged :) Is there anything I can do to help ? If I can, I would like to try to go the Wikimedia hackathon[1] at the end of May in Amsterdam to discuss about what should be done to the extension to have it integrated in wikipedia. But I'm not sure I will be in Europe at this time. I think that security is an important issue to cope with if you want a slight chance of seeing Jmol used. Nico [1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013 On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.il wrote: Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.il (the protein structure/function database) Proteopedia, http://proteopedia.org (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? - Switching between Jmol and JSmol depending on the browser capabilities - Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it - Opening Jmol in a new window, that would be scalable - Disabling javascript in Jmol script - ... - anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] FirstGlance in Jmol: Enhanced
I have today released a new version of FirstGlance in Jmol with many enhancements. http://firstglance.jmol.org as always. Formerly there was a single upper left control panel. Now there are 4 tabs in the control panel: Molecule (labeled with the PDB code), Views, Tools, and Resources. The Molecule tab is entirely new. It digests and summarizes a lot of information from the PDB file. Resolution and Free R are graded to assist those who are not structural biologists in interpreting them. Missing residues are reported chain by chain, including counts of charged residues that are missing. The initial view has been modified to include empty baskets in the regions where residues present in the crystal are missing in the model due to disorder. Thus you can no longer be unaware when there are missing residues. There is a clickable list of ligands and non-standard residues with their full names. The Find tool now supports finding sequences, e.g. sequence=rgd will highlight (and count) all Arg Gly Asp sequences present in all chains. Ditto for nucleotide sequences. The biological unit (quaternary structure) is more readily available and more help is provided. Former versions of FirstGlance reported no counts. This version reports counts of many things, including chains, amino acids, nucleotides (total and per chain), lengths of chains, missing residues, missing charged residues, numbers of each ligand/non-standard residue, disulfide bonds, and anything found with the Find tool. There are many new convenience features. A more complete list of enhancements is here: http://firstglance.jmol.org/versions.htm If you have suggestions for improvements, please do let me know! There are undoubtedly bugs. Please report anything that looks dubious, being sure to include the PDB code you were using. Eric P.S. I have not undertaken a JSmol version yet. /* - - - - - - - - - - - - - - - - - - - - - - - - - - - Eric Martz, Professor Emeritus, Dept Microbiology U Mass, Amherst -- http://Martz.MolviZ.Org Top Five 3D MolVis Technologies http://Top5.MolviZ.Org FirstGlance, used by Nature - http://firstglance.jmol.org 3D Wiki with Scene-Authoring Tools http://Proteopedia.Org Biochem 3D Education Resources http://MolviZ.org ConSurf - Find Conserved Patches in Proteins: http://consurf.tau.ac.il Atlas of Macromolecules: http://atlas.molviz.org Interactive Molecules in Public Spaces http://MolecularPlayground.Org Workshops: http://workshops.molviz.org - - - - - - - - - - - - - - - - - - - - - - - - - - - */ -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol extension for Mediawiki
Thank you for offering your help. Your expertise on Jmol extension will certainly become very handy. Regarding Wikipedia: Joel Sussman and myself took part of Wikimania 2011, and had the opportunity to meet and discuss with key MediaWiki developers and Wikipedia leaders. They got inside information on Proteopedia, it's integration with Jmol, and understood that Jmol never caused problems to Proteopedia. We offered our help and Proteopedia code. No progress after that. All this considering a Java based Jmol. I assume that today they might be more reluctant to using a Javascript centered JSmol. Still, we are willing to share our experience with Jmol/JSmol over MediaWiki in Proteopedia in case they changed their mind. Jaim On Apr 24, 2013, at 12:47 AM, Nicolas Vervelle wrote: Hi Jaime, Good to hear that you have kept working on this That would be great to have this packaged :) Is there anything I can do to help ? If I can, I would like to try to go the Wikimedia hackathon[1] at the end of May in Amsterdam to discuss about what should be done to the extension to have it integrated in wikipedia. But I'm not sure I will be in Europe at this time. I think that security is an important issue to cope with if you want a slight chance of seeing Jmol used. Nico [1] http://www.mediawiki.org/wiki/Amsterdam_Hackathon_2013 On Tue, Apr 23, 2013 at 5:36 PM, Jaime Prilusky jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il wrote: Hi Nico, It's good to know that you will have time for JSmol. I've done a lot on this direction, and Proteopedia is already rendering with JSmol when accessed from iPad. We are also displaying a static image while JSmol loads and renders the model, smoothly switching to the interactive model when done. Packaging everything and releasing a JSmol/Jmol extension for Mediawiki is on my list of tasks, although I've been busy on other Jmol related task. Jaim -- Dr Jaime Prilusky Head Bioinformatics RD Bioinformatics and Data Management Department of Biological Services Weizmann Institute of Science 76100 Rehovot - Israel eml: jaime.prilu...@weizmann.ac.ilmailto:jaime.prilu...@weizmann.ac.il fax: 972-8-9344113 tel: 972-8-9344959 OCA, http://oca.weizmann.ac.ilhttp://oca.weizmann.ac.il/ (the protein structure/function database) Proteopedia, http://proteopedia.orghttp://proteopedia.org/ (because life has more than 2D) On Apr 23, 2013, at 6:13 PM, Nicolas Vervelle wrote: Hi guys, I'm thinking on working again on the extension for integrating Jmol into a MediaWiki wiki. I haven't followed all the work that has been done recently on Jmol and JSmol. Do you have any links/explanations for me on what could be use for an integration into MW ? * Switching between Jmol and JSmol depending on the browser capabilities * Displaying a static image by default that could be replaced by a Jmol viewer when user clicks on it * Opening Jmol in a new window, that would be scalable * Disabling javascript in Jmol script * ... * anything you can think of Nico -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr ___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Try New Relic Now We'll Send You this Cool Shirt New Relic is the only SaaS-based application performance monitoring service that delivers powerful full stack analytics. Optimize and monitor your browser, app, servers with just a few lines of code. Try New Relic and get this awesome Nerd Life shirt! http://p.sf.net/sfu/newrelic_d2d_apr___ Jmol-users mailing list Jmol-users@lists.sourceforge.netmailto:Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
