Hi all. First, I did look at Proteopedia. This is really great but quite complex. We have to recognise that this use is what some people will be demanding on wikipedia once we get it started. I then e-mailed Tim Starling but he has not yet replied. I will copy this e-mail to him both as a reminder and as an indication about what we think is possible and desirable.
I think we should stick to uploaded files as these could go on Commons and be available to all wikimedia projects. Separate files, I presume as sub-pages of the page using the 3D jmol image, will be less general, but also more susceptable to vandals editing them and possibly adding dangerous code there. I will also contact one of the editors who is very involved with the chemicals infobox, and probably copy this e-mail to him at some stage also. Cheers, Brian. On Tue, May 26, 2009 at 09:05:20AM -0400, Jeff Hansen wrote: > Angel, > > This is a small point, but I personally don't like the idea of opening a > new window for the Jmol applet. It seems more aesthetically pleasing to > me to put the Jmol in a new div with a z-index that puts it in front of > the rest of the page. The div can be made draggable and resizable. > > > Jeff > > > *********************************************** > Jeff Hansen > Department of Chemistry and Biochemistry > DePauw University > 602 S. College Ave. > Greencastle, IN 46135 > jhan...@depauw.edu > *********************************************** > > > On May 26, 2009, at 7:30 AM, Angel Herr?ez wrote: > >> A little more on progress for Wikipedia support: >> >> I wrote: >> >>> I will try to do some experimenting over the weekend on the idea of a >>> template similar to chembox. I will use the Jmol Wiki (which of >>> course has the MediaWiki Extension and file type already set), so >>> that we have a better idea of what is workable from the Jmol side. >> >> Finally I could not use the Jmol Wiki since the version of MediaWiki >> there does not support what is needed. I got permission to do my >> tests at another wiki where they have both the Jmol Extension and an >> updated version of MW: >> http://www.sklogwiki.org/SklogWiki/index.php/User:AngelHerraez >> >> This is the summary. Feedback is welcome. >> >> 1. For a first go, set-up a simple version of Jmol implementation (no >> scripts) that integrates in the Chembox template (more precisely, >> Chembox_new) currently in WP. >> >> 2. The Chembox will include, within the 'Structure' subsection, a row >> entitled '3D structure' with a hyperlink that will open Jmol in a pop- >> up window (only if the user decides to go in). That's a resizable >> window with resizable JmolApplet filling 100%. Jmol popup menu and >> console are available as they are usually (but they could be >> restricted if so desired by editing the template, I think; anyway, I >> see no reason to do so) >> >> 3. The model file may come, depending on the wiki administrators' >> decision, either from an uploaded file (pdb, mol, xyz, etc. formats >> must be allowed for uploads in the wiki) or from a wikipage >> containing the molecular data. >> >> 4. Authors of wikipages need only >> 4a. Know how to use the Chembox (which is not totally trivial, but >> not difficult either, and not our problem) >> 4b. Insert this code (example): >> Cyclohexane.pdb >> into the pre-written field that says: >> 3DStruct = >> 4c. Make sure that the "Cyclohexane.pdb" file has been uploaded, or >> the "Cyclohexane.pdb" page has been created. >> >> >> Technical requirements: >> - MediaWiki 1.12 or later >> - Jmol MediaWiki Extension (preferably latest version, dated >> Dec.2008, r10478) >> - Permission to upload molecular files, if so chosen as the desired >> format >> - Either a simpler template, or the Chembox and all its accessory >> subtemplates from WP. Edition of some of these WP templates is needed >> to add the new 3DStruct parameter. >> - The new Chembox_3DStruct template. >> >> >> >> >> ------------------------------------------------------------------------------ >> Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT >> is a gathering of tech-side developers & brand creativity >> professionals. Meet >> the minds behind Google Creative Lab, Visual Complexity, Processing, & >> iPhoneDevCamp asthey present alongside digital heavyweights like >> Barbarian >> Group, R/GA, & Big Spaceship. http://www.creativitycat.com >> _______________________________________________ >> Jmol-users mailing list >> Jmol-users@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/jmol-users > > > > > ------------------------------ -- "One man alone can be pretty dumb sometimes, but for real bona fide stupidity there ain't nothing can beat teamwork." -- Mark Twain Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au ------------------------------------------------------------------------------ Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT is a gathering of tech-side developers & brand creativity professionals. Meet the minds behind Google Creative Lab, Visual Complexity, Processing, & iPhoneDevCamp as they present alongside digital heavyweights like Barbarian Group, R/GA, & Big Spaceship. http://p.sf.net/sfu/creativitycat-com _______________________________________________ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
