Hi Jonathan,
On Tue, Nov 23, 2010 at 8:59 PM, Jonathan Gutow <gu...@uwosh.edu> wrote:
> Nico,
>
> Bob can give you the details, but I think both things you suggest are
> possible. However, I see one big problem: in general I do not think
> we should default to opening a live Jmol in the wiki. A static
> picture which can then become a live Jmol is more appropriate. I
> think you want behavior more like the Jmol pop-in implemented by the
> export-to-web function. An example page is here:
>
> http://www.uwosh.edu/faculty_staff/gutow/Jmol_Web_Page_Maker/Export_to_web_tutorial.shtml
That's something similar that I had in mind :)
My idea is to simplify both the use of the Jmol extension and its
interaction with the user.
I can take care of PHP part of the coding (integration with MediaWiki
software), but I'd really appreciate any help for the other parts
(javascript, designing a nice HTML page displaying a molecule with Jmol and
controls, ...)
My current idea is the following :
- For inserting a possibility to view a chemical file in 3d in Wikipedia,
you just add something like <jmolFile>XXX.cml</jmolFile> in the Wikipedia
page.
- The Jmol extension renders it as a static display : a button, a link or
a still image. I will start with only a link or a button because it's a lot
easier. Using a still image will need more work, especially if I want to try
to generate it on the server dynamically.
- When the user clicks on the static display, a Javascript method is
called to create and display a complete HTML page with a Jmol applet and
useful controls and eventually informations.
If someone is interested in helping (writing also) for the Javascript method
and the HTML page, that would be really nice :)
My current ideas about the Javascript method arguments :
- The molecular data. For a beginning only as an URL, but later having
the ability to choose between URL or inline data.
- A simple title
- For later : a flag telling if it should use the unsigned or the signed
applet. For a beginning, always using the unsigned applet would be enough
- Bonus : Something optional about the kind of display (basic, protein,
crystal, ...) that could be used to customize the window displayed
My current ideas about the HTML page :
- Jmol applet (preferably resized with the window)
- Some controls letting the user easily do some actions on the molecule
(it could depend on the kind of display requested)
- Some informations about the molecule : name, number of atoms, ... (it
could also depend on the kind of display requested)
- Nice widgets ?
Anyone interested in contributing ?
Ideas are also welcome :)
Nico
> You can use the code in this page which is based on a template made by
> Angel. Note since this page was generated we have updated things to
> perform better. You would probably be best off generating a new page
> in Jmol and lifting the code from that.
>
> Jonathan
> On Nov 23, 2010, at 1:08 PM, Nicolas Vervelle wrote:
>
> > Hi,
> >
> > I have started working again on the extension to include Jmol in
> > Wikipedia.
> >
> > The current extension is not as simple as some Wikipedia people
> > would like (see this bugzilla report).
> > One idea there is that a Media handler for molecular files should be
> > developed (so that an image could be displayed automatically when
> > going on the page of a CML file). It's interesting but seems
> > complicated.
> >
> > I have an other idea that could be not really hard to develop but
> > would enable to show a lot of molecules easily.
> > But I need more infos on what Jmol is currently capable (I have lost
> > track and since I am no chimist at all that's difficult to follow).
> > The idea is to use a simple tag with only an identifier inside to
> > choose the molecule.
> > What do you think of the ideas below ?
> >
> > Can Jmol show a molecule having just a SMILES string ?
> > If so, what are the commands that need to be executed ?
> > I think we could add a syntax for Wikipedia where a user would
> > simply have to add something like <smiles>XXXX</smiles> to display
> > the molecule in Jmol.
> >
> > Also, can Jmol retrieve a molecular file using only an identifier
> > (like getting the molecule on the pdb database) ?
> > What are the options and the commands ?
> > That would allow the same kind of addition : <pdb>XXXX</pdb> to
> > display a molecule from the pdb database.
> >
> > Nico
>
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