Re: [Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
On 16 Jul 2006 at 10:58, Brian Salter-Duke wrote: Hi Angel, Great. Did you write all that lot in response to my question? These Well, yes. Just as I was reading your message, I had the very clear idea that this was easy to do, so I **had** to go and do it --instead of the planned Saturday morning task of doing some cleaning on the house, so merit is reduced ;-) --. Then I got hooked on improving it, that's why there are 5 versions (really, only 2 methods, nr.1 with pop-up and nr. 2 with inline frame which later I went polishing). I am sure this will be of use for me too at some time; I am always worried about the delay in Jmol loading, form the user interface point of view. options are really just what I think is needed. I'm impressed if not overwhelmed. I will try to use these in the Jmol wiki. I may point a few people to your site to have a look too. Good. Although it is a testing area URL, I will try to leave it there. Finally, the actual location of Jmol files, molecules and images have to be modified in the code, although this is easy. What has still to be tested is the suitability of this code to be integrated within Wikipedia, which I assume has automatic backends, database integration and so on. That's why I went on versions 4 and 5 trying to make the code as portable and generalizable as I could, thinking on not-hand-made pages and different molecules. The setup is so: - A single, common file Jmol_frame.htm holds the applet and the desired controls -like spin on/off, spacefill, sticks, etc.- This page points to Jmol.js and the JmolApplet files. - A single, common file Jmol_caption.htm holds the message being shown by default, which in v.5 also includes a still image (taken manually by screen capture of the Jmol view). - The page itself where the contents are, invokes Jmol_caption.htm via IFRAME SRC="" and invokes Jmol_frame.htm via a _javascript_ function that receives the molecule's filename and displayed name. The size of the applet is specfiied also in this page via a variable JmolSize that will be read by Jmol_frame. - Fonts, colors, etc. can be changed by editing the code in a couple of places. This could also be centralized via _javascript_ variables, so that the 2 common files need not to be changed. On the other hand, I wouldn't think this way of integration will be any difference regarding security, or lack of it (with respect to other integration methods like the MediaWiki extension). Please, anyone do give any ideas as to which featuures would be interesting to add. - 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=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
Really great Angel, I like option 5 a lot. I will try to add it to the MediaWiki extension (with a few fixes also to the extension) as soon as I manage to find some time. Nico Angel Herraez wrote: Brian, I have written a small prototype of how this could be done. The files, including Jmol files, sum up 845 kb, so I am not sending it to the list You can test it at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.htm If you prefer, you can get it all zipped at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.zip It can be polished; tell me what you miss - 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=lnkkid=120709bid=263057dat=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=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
On Sun, Jul 16, 2006 at 03:44:36PM +0200, Nicolas Vervelle wrote: Really great Angel, I like option 5 a lot. I will try to add it to the MediaWiki extension (with a few fixes also to the extension) as soon as I manage to find some time. That would be great, Nico. I hope you can find the time. I replied to Angel privately but my message was included in one from him to the list. However let me add to that publically on the list to thank Angel for this excellent and rapid response to my question. I am sure that this will be a great help to establishing use of Jmol in Wikipedia. I too like option 5, but I am not sure what the constraints on the pdb image shown are. We might want a choice of image here including the chemdraw like images that are currently widely used in chemistry articles on wikipedia. In some cases we might want just a specific paragraph of text rather than an image. Are these possible? I agree that option 1 popups are annoying but some people like them. If we implement option 1 for wikis, I think we need to allow n popups at once if there are n Jmol images from the page. As Angel wrote it, option 1 shows a page with two molecules but clicking the second replaces the image in the first popup. In practice we would want to have 2 popups side by side for comparision. Personally I would allow just option 5 - allowing image - and option 4 - replace box with no image with Jmol object. Cheers, Brian. Nico Angel Herraez wrote: Brian, I have written a small prototype of how this could be done. The files, including Jmol files, sum up 845 kb, so I am not sending it to the list You can test it at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.htm If you prefer, you can get it all zipped at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.zip It can be polished; tell me what you miss - 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=lnkkid=120709bid=263057dat=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=lnkkid=120709bid=263057dat=121642 -- ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users End of Jmol-users Digest, Vol 2, Issue 12 * -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] - NB New! Old still works Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm 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=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
Re: [Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
Brian, I have written a small prototype of how this could be done. The files, including Jmol files, sum up 845 kb, so I am not sending it to the list You can test it at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.htm If you prefer, you can get it all zipped at http://biomodel.uah.es/pruebas/jmol/pop-up_Jmol/pop-up_Jmol.zip It can be polished; tell me what you miss - 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=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
[Jmol-users] Delaying loading the web applet - re Jmol on Wikipedia
As I have mentioned before I am trying to get Jmol up and running on Wikipedia. It seems that my Wikipedia technical admin friend raised this on IRC and asked people to look at how it all worked on, I guess, the Jmol wiki. They concluded that WP users expect pages to come up immediately and that WP users would be put off by the slowness of loading the Jmol applet. He suggested to me that what was needed was something like this:- When the page comes up, it has a large box that says Clicking here will bring up a 3-dimensional image of the molecule that you can manipulate. It uses the Jmol applet. This may take quite a time to download if you do not already have it in cache. If you want to use the Jmol image, click here or rather better words expressing this. The box could perhaps give a clue about the Jmol image by have a 2-dimensional jpg or whatever image. Clicking on that box would bring up Jmol replacing the box on the page. Is this possible, perhaps using javascript? If so, can anybody smarter than I at javascript write something, so we can test it on the Jmol wiki? I am sure that this or something like it will make the introduction of Jmol to Wikipedia more acceptable to the Wikipedia administrators. However, it is not holding back a test of Jmol on Wikipedia. That is being delayed for other reasons - good reasons. While this delay is going on, we could perhaps improve the way Jmol might be used on Wikipedia pages. I welcome comment and assistance. Brian. -- Brian Salter-Duke (Brian Duke) [EMAIL PROTECTED] - NB New! Old still works Post: 626 Melbourne Rd, Spotswood, VIC, 3015, Australia Phone 03-93992847. http://www.salter-duke.bigpondhosting.com/brian/index.htm 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=lnkkid=120709bid=263057dat=121642 ___ Jmol-users mailing list Jmol-users@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/jmol-users
