Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
Bob Hanson wrote: fascinating! Comments: 1. I suggest be Ok 2. : Size of the applet. Does that mean it's always square? Currently, yes. But that would be a thing to add. 3. Two valuable options we should probably consider building into Jmol for this sort of public use might be: a) allowPopUpConsole b) allowShowFile realizing that a wiki may involve somewhat more control over the environment than a web site. Personally I've never been too thrilled with "show file" and its ability to deliver into the user's hands any file on the system. I am not sure about this: wikis are designed to be open, so even the files that are put there are openly accessible and can be changed by users. 4. One could imagine a system-wide defaultScript option. Yes Thanks for the ideas, Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
Bob Hanson wrote: Nico, you need a random number in that "windowTitle" variable. This is necessary because one needs to make sure that the window really DOES pop up -- if the user has hidden a previously popped up window and then press the button again (currently), then "nothing" (visible) happens. Actually, I think the window is loaded, but it doesn't come forward. So the classic solution to this is to assign a unique number in that second parameter of open(). Ok, I will add it this evening. Thanks Bob Nicolas Vervelle wrote: Hi everyone, I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Check the full description : http://wiki.jmol.org/index.php/MediaWiki and a simple example page: http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension Comments are welcome :) Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
On Wed, Apr 26, 2006 at 11:37:51PM +0200, Egon Willighagen wrote: > On Wednesday 26 April 2006 22:26, Nicolas Vervelle wrote: > > I have finished a first version of a fully functional version of a > > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > > well-known Wikipedia). > > Looks good! > > Anyone who knows where to start lobbying to get this included in WikiPedia? I have been discussing this with one of the senior Wikipedia developers but waiting until Nico had completed his extension. I will follow up on this today. I have only just seen the news this morning here in Australia. See:- http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_models and its talk page, where is information from Nico and others. I hope we can get a trial on Wikipedia soon. Cheers, Brian. > Egon > > -- > CUBIC > blog: http://chem-bla-ics.blogspot.com/ > > > --- > Using Tomcat but need to do more? Need to support web services, security? > Get stuff done quickly with pre-integrated technology to make your job easier > Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 > ___ > Jmol-users mailing list > Jmol-users@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/jmol-users -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://members.iinet.net.au/~linden1/brian/ Honorary Researcher Fellow, Dept. of Medicinal Chemistry, Monash Univ. --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
Nico, you need a random number in that "windowTitle" variable. This is necessary because one needs to make sure that the window really DOES pop up -- if the user has hidden a previously popped up window and then press the button again (currently), then "nothing" (visible) happens. Actually, I think the window is loaded, but it doesn't come forward. So the classic solution to this is to assign a unique number in that second parameter of open(). Bob Nicolas Vervelle wrote: Hi everyone, I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Check the full description : http://wiki.jmol.org/index.php/MediaWiki and a simple example page: http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension Comments are welcome :) Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
fascinating! Comments: 1. I suggest be 2. : Size of the applet. Does that mean it's always square? 3. Two valuable options we should probably consider building into Jmol for this sort of public use might be: a) allowPopUpConsole b) allowShowFile realizing that a wiki may involve somewhat more control over the environment than a web site. Personally I've never been too thrilled with "show file" and its ability to deliver into the user's hands any file on the system. 4. One could imagine a system-wide defaultScript option. Nicolas Vervelle wrote: Hi everyone, I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Check the full description : http://wiki.jmol.org/index.php/MediaWiki and a simple example page: http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension Comments are welcome :) Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users -- Robert M. Hanson, [EMAIL PROTECTED], 507-646-3107 Professor of Chemistry, St. Olaf College 1520 St. Olaf Ave., Northfield, MN 55057 mailto:[EMAIL PROTECTED] http://www.stolaf.edu/people/hansonr "Imagination is more important than knowledge." - Albert Einstein --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Jmol applets in MediaWiki and Wikipedia
On Wednesday 26 April 2006 22:26, Nicolas Vervelle wrote: > I have finished a first version of a fully functional version of a > MediaWiki extension to add Jmol applets in MediaWiki wikis (like the > well-known Wikipedia). Looks good! Anyone who knows where to start lobbying to get this included in WikiPedia? Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] AtomIterator field important for 'select protein'?
On Wednesday 26 April 2006 07:42, Egon Willighagen wrote: > Which AtomIterator field need to be setup correctly to have Jmol detect > atoms as protein atoms? The important field turned out to be the group3 field. A screenshot of the state of Bioclipse today is at: http://bioclipse.net/ I think I mentioned it before, but will do it again to make sure :), it has a built in script editor with code completion and syntax highlighting. The screenshot shows a file browser on the left, the console below the Jmol window and enzyme properties on the right. It currently has no AtomSetChooser, but that might follow soon. Binaries can be downloaded form bioclipse.sf.net, and the source is available from SVN, and easiest run from Eclipse. Egon -- CUBIC blog: http://chem-bla-ics.blogspot.com/ --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Jmol applets in MediaWiki and Wikipedia
Hi everyone, I have finished a first version of a fully functional version of a MediaWiki extension to add Jmol applets in MediaWiki wikis (like the well-known Wikipedia). Check the full description : http://wiki.jmol.org/index.php/MediaWiki and a simple example page: http://wiki.jmol.org/index.php/Jmol_MediaWiki_Extension Comments are welcome :) Nico --- Using Tomcat but need to do more? Need to support web services, security? Get stuff done quickly with pre-integrated technology to make your job easier Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo http://sel.as-us.falkag.net/sel?cmd=lnk&kid=120709&bid=263057&dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
