Wikipedia talk:Using Jmol to display molecular models

Please contact also the 'Blue Obelisk Movement'

You should contact people from the Blue Obelisk Movement. Possible extensions and possibilities of the actual ideas would be:

• using JChemPaint which uses the CDK to edit structures and visualize them in 2D.
• storing structures and meta data in Chemical Markup Language, e.g. boilding points, etc.
• Categorizing every data would allow some fancy mining ideas.

JKW 18:00, 8 April 2006 (UTC)

Comments and suggestions on the Jmol Extension ?

Then, please add them directly in the discussion page dedicated to the Jmol Extension on MediaWiki in the Jmol Wiki. NicoV 20:55, 8 April 2006 (UTC)

All right JKW 22:42, 8 April 2006 (UTC)

I dropped an e-mail on the Blue Obelisk mailing list that your recommended page should be used to exchange all ideas, technical issues, and everything else which is necessary to get Jmol and other chemical tools to work together with Mediawiki. JKW 23:01, 8 April 2006 (UTC)

I entirely agree that all discussion about Jmol and MediaWiki should take place at the Jmol Wiki discussion page. Wikipedia:Using Jmol to display molecular models is concerned with how we use Jmol on Wikipedia, but the next step is to get the applet and scripts installed on the Wikipedia servers. I am waiting until NicoV has completed the current extensions before trying to get this done. JKW - thanks for alerting to me on my talk page to the edits all over that had occurred while I slept on the the other side of the world. --Bduke 01:52, 9 April 2006 (UTC)

Just to be really clear on this! Especially in the area of small molecules there is still a huge problem with collecting high quality data, since many people have many ideas which properties are the 'real' properties. Since there was and still is a huge Cheminformatics community forcing more open standards, open data, and open access I hope really that Wikipedia supports all those efforts.

Means, beside the visualization Wikipedia or other Mediawiki servers might become THE standard for storing and collecting data in a highly verbose and open way. This is especially in this area crucial, since for example Mediawiki talk pages might be used to establish a common view why some properties are preferred in favour of others. This is true knowledge building!

I am really looking forward for any positive' news in this direction.

JKW 21:04, 10 April 2006 (UTC)

Jmol extension is really useful --Pansanel 07:49, 11 April 2006 (UTC)

Many molecular structures are difficult to handle in 2D sketch. A 3D visualization software is great for this job. For example, calixarene derivatives have a cone shape. Such molecule can really better understand with a 3D interactive tool.

To keep you informed (check the current status on the official page and the example page for the Jmol Extension :

• I have redesigned the Jmol Extension this weekend (much cleaner source code) and the new format (only <jmol> tags) is working. I will start working on the other ideas. --NicoV 21:44, 10 April 2006 (UTC)
• Support for loading molecular models from an URL added (21:21, 12 April 2006 (UTC)), from a wiki page added (13:59, 15 April 2006 (UTC)), from files uploaded in the wiki added (16:00, 17 April 2006 (UTC)). I think I have finished with implementing the possibilities of loading data into Jmol.
• An addition that I think would be useful for the Wiki: rather than directly adding a Jmol applet in a MediaWiki page (which requires loading the applet when viewing the page), I have added the possibility to add a button opening a new window with the Jmol applet in it (the applet will only be loaded for people that want to see the molecule in 3D).

--NicoV

Brilliant idea. I love it. --Bduke 22:00, 24 April 2006 (UTC)

• Other additions: links, links that open a popup window, checkboxes, menus, radio groups.

I have finished the features I wanted to add for a first functional version of the Jmol extension. Comments (and tests) are welcome in the official talk page for the extension.

How are we to use Jmol on Wikipedia?

I hope to have Jmol installed on Wikipedia soon, when NicoV's extension stabalises. How are we use the various options he has given us? We could:-

• Add molecular coordinates in page.
• Add molecular coordinate files as a wiki page such as a sub page of the article page.
• Upload the files to somewhere on Wikipedia or on Commons.

Let us debate this before starting to use it. The first two options are illustrated at my user page on the Jmol wiki. --Bduke 22:21, 17 April 2006 (UTC)

The third option is illustrated at this page, and you can see the possibility of categorizing the molecular data in this category page. --NicoV 04:20, 18 April 2006 (UTC)

My own thoughts:

• Option 1 would clutter the edit if used for other than very small molecules.
• Between option 2 and 3, I don't know. Option 3 enables the use of gzipped files which can be interesting for very big files, but all files will be stored in the Image namespace (but categories can still be used). --NicoV 20:35, 27 April 2006 (UTC)

I have one concern about putting files in the image space. We are likely to be pestered by bots who check for allowed use of images. We will get deletions of files and messages on our talk pages warning us about the files we have uploaded. I will talk to the WP technical guy about this. I think a lot of files will be small and can go "inline" (option 1). Larger ones could use option 2. Maybe only those used in several places should use option 3. --Bduke 22:08, 27 April 2006 (UTC)

Settings for Jmol images on Wikipedia

I am trying to initiate discussion on settings we should use for 3D images on the Structure Working group talk page. Could this group suggest what should be used? We should make sure things harmonise well with what we are doing with other 3D image formats. I know very little about this, can you guys advise? Thanks, Walkerma 16:58, 27 April 2006 (UTC)

Recent progress

While it is a long time since this project was last mentioned, it has not been forgotten. The problem has been that the Jmol extensions for MediaWike are not thought to be sufficiently secure for the Wikipedia Technical folk. The author of the Jmol extension for MediaWiki has been too busy, and, like me, too ignorant of the security issues, to fix this. However, I am now reasonably confident that it will be fixed before too long. Other issues are:-

Media for Jmol data

The extension has several ways of having the data ready for Jmol as detailed here:-

1. Data being an uploaded file like image files.
2. Data being a standard wiki page or sub-page.
3. Data being inline in the page calling Jmol.
4. Data being a URL of a file on another server.

I do not see the WP techs supporting 4. It seems to me that we should be using (1) and getting the system to treat data files just like images. The extension also supports showing the Jmol image in a pop-up window. I strongly support this for WP as downloading the applet can be slow and we do not want people to download it not knowing they do so when they just click on a link. --Bduke (talk) 06:43, 14 December 2007 (UTC)

The pop-up window is shown here. --Bduke (talk) 06:59, 14 December 2007 (UTC)

My User page on the Jmol Wiki here shows a pop-up window and an example of how a Jmol image can appear in a paragraph like images do. --Bduke (talk) 07:25, 14 December 2007 (UTC)

Wikiversity

I particularly want to get Jmol working on Wikiversity as it is widely used in educational materials on computational chemistry including some we are planing to put on to Wikiversity. The appropriate format for the Jmol data here is I think the uploaded file. This points to a later development of uploading data file to Commons. --Bduke (talk) 06:59, 14 December 2007 (UTC)

Is this the time?

There has been renewed interest on this on the Jmol list, with recent discussion suggesting that use be enabled within the chemical infobox. The security issues appear to have been resolved. A really good example of the use of the Jmol extension on a wiki is on Proteopedia here. Details of the jmol email list are here. You will also find examples of the use of the extension on the Jmol Wiki itself. We need to convince the WMF techs to install the jmol mediawiki extension, so we need to show that we want this. I think this is the time to make a determined push to get it installed. --Bduke (Discussion) 22:45, 26 May 2009 (UTC)

This is great news but will only work if developers of the Wikipedia extension and of Jmol are actively and committedly working on it and monitoring the introduction closely. I have a few questions/suggestions:

1. Is there already a server side script that automatically creates and caches images to display as a fallback?
2. Any code (e.g. JavaScript) execution by the applet must be prevented, preferably by stripping such functionality from the script applet at all. For security reasons it might possibly a good idea to restrict file formats by stripping the applet.
3. A related issue is the loading of files from external servers. This option must be eliminated, preferably by hard-coding and code elimination
4. As a Jmol feature request (and possible standard display mode on Wikipedia!) I would like to see a style that mimics normal skeletal structures (black on white, solid lines, implicit hydrogens, heteroatom symbol display). Common editors such as ChemDraw can do this.

Cacycle (talk) 00:59, 27 May 2009 (UTC)

The first step is getting the WMF techs on side. Once it is installed, then I believe the Jmol people will monitor closely. To your questions:

1. I do not know, but I think the idea is is to have an ordinary image there and a button to click to bring up the jmol image, so it will not come up by default and there will still be an image there.
2. If I understand you correctly I think that will be done.
3. Loading files from external servers is certainly a no-no. In fact it might only use uploaded files, with a restricted set of file extensions approved.
4. Perhaps you should raise this on the Jmol list.

I might add that I have nothing to do with the jmol wikimedia extension, although I have tried it out. I have been pushing this for years, but have not had much support. I am mainly acting as a link between the jmol list and wikipedia. It is certainly going to need support from those who work on chemical infoboxes. --Bduke (Discussion) 02:54, 27 May 2009 (UTC)

1. The default/preview/fallback image should be automatically generated server-side so that we do not have to waste time on doing this by hand

Cacycle (talk) 04:13, 27 May 2009 (UTC)

How? It is quite distinct from the jmol extension. Maybe I am not understanding you. --Bduke (Discussion) 06:45, 27 May 2009 (UTC)

I suggest to have a still image as a preview and fallback for no-Java enabled browsers displayed. This image should be a preview of what you see in the applet, i.e. a rendered molecule image. You could create these by hand by creating a screenshot, edit it, upload it, and embed it by hand for every change done to the molecule. The server side Jmol extension should take care of this. Cacycle (talk) 13:55, 27 May 2009 (UTC)

A little feedback, from my Jmol side and some experience with design of the Extension: (--AngelHerraez (talk) 17:09, 7 June 2009 (UTC))

1. Although the Jmol application has the capability to generate a snapshot, having that done in the server is going to be hard if even possible. I don't think we can aim for that now, it's a wholly separate business. We will have to be content with a link or button; or the page editor may insert his own image as a link.

2. That is already implemented in the Extension: the inserted applet will not execute any Javascript. File formats can hardly be restricted, since Jmol uses plain text or gzipped files, but does not rely on their extension. But again, there is no way an arbitrary file will be executed; only supported formats will produce an output in the form of a molecular model.

3. Loading from external servers is disabled by Java security, as long as the unsigned applet is used (which is the default and may be the only choice per the Wiki administrators decision in configuring the Extension).

4. That is certainly feasible using Jmol scripting, but I don't see why a 3D model should be made look as a 2D drawing. We can discuss the details though.

As I see it, we have two possible ways of having Jmol applets in WP, at least for the first stage:

• The full use of the Extension by editors who have learned to use its markup. That will allow applets and controls acting on them, opening basically the full potential of Jmol. The applets would load with the page, which delays the page load and should be used only with a previous warning for the visitors (like e.g. on a previous page).
  • As a sub-choice, such editor may choose to include only applets in pop-up windows (using the Extension standard methods) that are opened by the user clicking on a link or button. That avoids any undesired delays, avoids taking space from the page, and allows to warn the visitor, but limits the interaction with the model since no controls can be inserted in the popup. In addition, some people don't like popups (I want to research into inline possibilities)
• The second way is to implement a simpler way of inserting a JmolApplet that uses the Extension internally. An example is the proposed implementation as part of the ChemBox. The editor will need to learn how to use the ChemBox and its particular syntax for Jmol, which could be as simple as the model's file name or page name. The applet would show in a popup, and the warning can be preprogrammed into the Chembox. You can see an example. — Preceding unsigned comment added by AngelHerraez (talk • contribs)

Some valuable insight here. Thanks, Angel. I like the Chembox example, and I think we should aim to get that implemented first, although making it clear to the tech people, that there will be demand for other uses. I am not clear where the pdb file is and how it is installed. I would also comment that while Jmol does not use extensions, file upload on wikipedia or Commons does. We would have to add the pdb file extensions and others to the allowed file types for upload.

In the example at SklogWiki the model files are put as content of pages (maybe in a specific space within the wiki, not sure); they have decided that instead of uploading the files, but either way should not make a difference regarding functionality.

I know about authorizing extensions for upload. What I mean is that even if only PDB was authorized, anyone could upload an XYZ file renamed as PDB. I don't think that a checking can be run on those file formats (as it is done, if I reckon correctly, on images, not only based on extension but on content).

I am doing progress with using a link to have the applets inserted into the page, rather than in a pop-up window. I hope to demo that soon once the JmolWiki engine and Extension have been updated.

Ideas about most desirable formats are welcome. --AngelHerraez (talk) 18:55, 8 June 2009 (UTC)