On Thu, May 21, 2009 at 05:51:46PM +0200, Angel Herr?ez wrote:
> Chris Foley wrote:
>
> > I think this has great potential but I don't like applets appearing
> > in my web pages if I don't want/expect it
>
> Right. The discussion has always being on the idea that the applet
> should load only when the user chooses so. One option is an image (if
> we could manage to have it generated by the server, which is
> unlikely), another is a link or button.
> I personally like the idea of Jmol being part of the ChemBox (I guess
> it is called something like that). Some chemicals have links to
> PubChem, or expansible boxes with formulas, details, etc. There could
> be a link like "see in 3D" that would open the Jmol applet either
> inline or in a separate page as Chris proposes.
>
> For example, the Toluene page has this, using Template:Chembox
>
> {{chembox
> | Name = Toluene
> | ImageFileL1 = Toluol.svg
> | ImageSizeL1 = 80px
> | ImageFileR1 = Toluene-from-xtal-3D-balls.png
> | ImageSizeR1 = 150px
> | OtherNames = phenylmethane<br/>toluol<br/>methylbenzene
> | Section1 = {{Chembox Identifiers
> | SMILES = Cc1ccccc1
> | CASNo = 108-88-3
> | ChemSpiderID = 1108
> | RTECS = XS5250000
> }}
> | Section2 = {{Chembox Properties
> | Formula = C<sub>7</sub>H<sub>8</sub>
> (C<sub>6</sub>H<sub>5</sub>CH<sub>3</sub>)
> | MolarMass = 92.14 g/mol
> | Appearance = Clear colorless, liquid
> | Density = 0.8669 g/mL, liquid
> | Solubility = 0.47 g/l (20-25?C)
> | MeltingPt = -93 ?C
> | BoilingPt = 110.6 ?C
> | Viscosity = 0.590 c[[Poise|P]] at 20?C
> }}
> | Section3 = {{Chembox Structure
> | Dipole = 0.36 [[Debye|D]]
> }}
> | Section7 = {{Chembox Hazards
> | ExternalMSDS = [http://www.sciencelab.com/xMSDS-Toluene-9927301
> ScienceLab.com]
> | MainHazards = highly flammable
> | NFPA-H = 2
> | NFPA-F = 3
> | NFPA-R =
> | FlashPt = 4 ?C/ 39.2 ?F
> | RPhrases = {{R11}}, {{R38}}, {{R48/20}}, {{R63}}, {{R65}},
> {{R67}}
> | SPhrases = {{S2}}, {{S36/37}}, {{S29}}, {{S46}}, {{S62}}
> }}
> | Section8 = {{Chembox Related
> | Function = [[aromatic hydrocarbon]]
> | OtherFunctn = [[benzene]]<br/>[[xylene]]<br/>[[naphthalene]]
> | OtherCpds = [[methylcyclohexane]]}}
> }}
>
>
> How about a new parameter for Jmol inside {{Chembox Structure ?
>
I think this is a brilliant idea.
I come at this from the wikipedia side as I certainly spend more time
there than with jmol. The difference between the English wikipedia and
all other wikis is that it is massively larger. This makes the technical
people, like Tim Starling, rather conservative about what they allow. I
think we have to start small. Doing as you suggest pretty well leaves
the jmol insertions to the people in WikiProject Chemicals (I am not
active there, only on its parent project WikiProject Chemistry) who will
know what to do. They will iron out initial bugs. Then we should
restrict the use to file upload. Images are now called "File:..", not
"Image:..", so this makes it easy to add more file extensions to handle
pdb files etc. Such files could be uploaded to Commons to be available
on all WMF projects. That would involve working with the Commons
community. I suggest we limit the number of file extensions initially.
I will look at proteopedia over the weekend and then e-mail Tim
Starling, who I know and who is in Australia. It is a few years since I
last discussed it with him. I'll try to find out what he thinks needs to
be done. Has Gerard approached anyone?
Earlier, I suggested a trial on wikiversity. I started putting up some
web course materials there on computational chemistry over a year ago,
but have been distracted by other things. I have one module that uses
Jmol (or Rasmol, or Chime earlier) extensively. I am prepared to put all
that up as a trial of Jmol on wikiversity if the WMF techs allow it.
Nevertheless, the quicker we get it on wikipedia the better. There will
however be issues about adding it to all language wikipedia. Maybe only
the english wikipedia and perhaps a few others such as the German and
French wikipedias have the chemistry editor base to use Jmol well and
not create trouble for the techs.
I am happy to act as a facilitor between the Jmol community and the
English Wikipedia community (and perhaps the Commons community),
particularly the WikiProject Chemistry
(http://en.wikipedia.org/wiki/Wikipedia:WikiProject_Chemistry).
Take a look at:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_models
It has had few edits since May 2007. Leap in and add your ideas there.
Some of the WikiProject Chemistry folks will have it on their watchlist
and notice the new activity.
Brian.
--
The problem with defending the purity of the English language is that
English is about as pure as a cribhouse whore. We don't just borrow words;
on occasion, English has pursued other languages down alleyways to beat
them unconscious and riffle [sic] their pockets for new vocabulary
-- James D. Nicoll
Brian Salter-Duke (Brian Duke) Email: b_duke(AT)bigpond(DOT)net(DOT)au
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