Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
CML (http://cml.sourceforge.net) is open XML-based format so we could allow it on Commons and provide files repository for other projects (such as Kalzium).
There is also Java-based open source viewer JMol (http://jmol.sourceforge.net) including web browser plugin. With JMol we could dramatically enreach chemistry/biochemistry related pages in Wikipedia/Wikibooks/Wikiversity in same way as we support Ogg media files playback now.
Eugene.
2008/11/26 Eugene Zelenko eugene.zelenko@gmail.com:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
How does it know how to render say cyclohexane?
Hi!
On Tue, Nov 25, 2008 at 7:58 PM, geni geniice@gmail.com wrote:
2008/11/26 Eugene Zelenko eugene.zelenko@gmail.com:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
How does it know how to render say cyclohexane?
See sample files in http://websvn.kde.org/trunk/KDE/kdeedu/kalzium/data/molecules/.
-- geni
Eugene.
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
2008/11/26 Eugene Zelenko eugene.zelenko@gmail.com:
See sample files in http://websvn.kde.org/trunk/KDE/kdeedu/kalzium/data/molecules/.
Yes most of those have fairly obvious low energy positions. With cyclohexane how do you tell the system the difference between chair and twisted boat cyclohexane?
On Wed, Nov 26, 2008 at 2:59 PM, Eugene Zelenko eugene.zelenko@gmail.com wrote:
Hi!
On Tue, Nov 25, 2008 at 7:58 PM, geni geniice@gmail.com wrote:
2008/11/26 Eugene Zelenko eugene.zelenko@gmail.com:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
How does it know how to render say cyclohexane?
See sample files in http://websvn.kde.org/trunk/KDE/kdeedu/kalzium/data/molecules/.
Once upon a time, I had suggested to render SMILES [1] from wikitext: <smiles>N[C@H](C)C(=O)O</smiles> for D-alanine
Bur, conversion seems to be tricky, and I didn't find a straightforward way to convert them to PNG with free software.
So, uploading chemicals as CML seems to be a sensible option. It would be more flexible, though it will take more time/knowledge to create CML files.
We might want to think about "embracing and extending": <name convention="wikipedia">Methane</name>
A Java-Plugin is fine, as long as we render PNGs by default. I for one don't want to wait for Java to load and grab my resources each time I see a Wikipedia page with a molecule...
Cheers, Magnus
[1] http://www.daylight.com/dayhtml/doc/theory/theory.smiles.html
On Tue, 25 Nov 2008 19:03:12 -0800, Eugene Zelenko eugene.zelenko@gmail.com wrote:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
CML (http://cml.sourceforge.net) is open XML-based format so we could allow it on Commons and provide files repository for other projects (such as Kalzium).
There is also Java-based open source viewer JMol (http://jmol.sourceforge.net) including web browser plugin. With JMol we could dramatically enreach chemistry/biochemistry related pages in Wikipedia/Wikibooks/Wikiversity in same way as we support Ogg media files playback now.
See:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_model...
I have been trying off and on over a couple of years to get this on wikipedia. There is a mediawiki extension but it appears to have security issues. It needs someone to address these issues. Personally I would like to see Jmol on wikiversity and that might be a suitable trial before it goes on wikipedia.
More later in this discussion. I must run.
Brian.
Eugene.
Hoi, I remember that when the security issues were discussed, I did contact the people who created the extension. I was told at the time that they would look into this. The question I have, is this security issue still relevant ? Thanks, GerardM
2008/11/28 Brian Salter-Duke b_duke@bigpond.net.au
On Tue, 25 Nov 2008 19:03:12 -0800, Eugene Zelenko < eugene.zelenko@gmail.com> wrote:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
CML (http://cml.sourceforge.net) is open XML-based format so we could allow it on Commons and provide files repository for other projects (such as Kalzium).
There is also Java-based open source viewer JMol (http://jmol.sourceforge.net) including web browser plugin. With JMol we could dramatically enreach chemistry/biochemistry related pages in Wikipedia/Wikibooks/Wikiversity in same way as we support Ogg media files playback now.
See:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_model...
I have been trying off and on over a couple of years to get this on wikipedia. There is a mediawiki extension but it appears to have security issues. It needs someone to address these issues. Personally I would like to see Jmol on wikiversity and that might be a suitable trial before it goes on wikipedia.
More later in this discussion. I must run.
Brian.
Eugene.
-- Brian Salter-Duke b_duke@bigpond.net.au [[User:Bduke]] mainly on en:Wikipedia. Also on fr: Wikipedia, Meta-Wiki and Wikiversity and others. Go Wikimedia Australia Inc, Go!
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
Hi!
On Fri, Nov 28, 2008 at 3:43 AM, Gerard Meijssen gerard.meijssen@gmail.com wrote:
Hoi, I remember that when the security issues were discussed, I did contact the people who created the extension. I was told at the time that they would look into this. The question I have, is this security issue still relevant ?
I think will be good idea to ask Brion, Tim and other developers to make extension's code review. Not only form security point of view but also other suggestions for improvement may appear.
Is it included in translate wiki? :-)
Thanks, GerardM
Eugene.
2008/11/28 Brian Salter-Duke b_duke@bigpond.net.au
On Tue, 25 Nov 2008 19:03:12 -0800, Eugene Zelenko eugene.zelenko@gmail.com wrote:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
CML (http://cml.sourceforge.net) is open XML-based format so we could allow it on Commons and provide files repository for other projects (such as Kalzium).
There is also Java-based open source viewer JMol (http://jmol.sourceforge.net) including web browser plugin. With JMol we could dramatically enreach chemistry/biochemistry related pages in Wikipedia/Wikibooks/Wikiversity in same way as we support Ogg media files playback now.
See:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_model...
I have been trying off and on over a couple of years to get this on wikipedia. There is a mediawiki extension but it appears to have security issues. It needs someone to address these issues. Personally I would like to see Jmol on wikiversity and that might be a suitable trial before it goes on wikipedia.
More later in this discussion. I must run.
Brian.
Eugene.
-- Brian Salter-Duke b_duke@bigpond.net.au [[User:Bduke]] mainly on en:Wikipedia. Also on fr: Wikipedia, Meta-Wiki and Wikiversity and others. Go Wikimedia Australia Inc, Go!
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
Hoi, JMOL is currently not part of the Betawiki effort. It could be when it makes sense to do so. It makes sense to do so when it is safe to run. Thanks, GerardM
2008/11/28 Eugene Zelenko eugene.zelenko@gmail.com
Hi!
On Fri, Nov 28, 2008 at 3:43 AM, Gerard Meijssen gerard.meijssen@gmail.com wrote:
Hoi, I remember that when the security issues were discussed, I did contact
the
people who created the extension. I was told at the time that they would look into this. The question I have, is this security issue still
relevant ?
I think will be good idea to ask Brion, Tim and other developers to make extension's code review. Not only form security point of view but also other suggestions for improvement may appear.
Is it included in translate wiki? :-)
Thanks, GerardM
Eugene.
2008/11/28 Brian Salter-Duke b_duke@bigpond.net.au
On Tue, 25 Nov 2008 19:03:12 -0800, Eugene Zelenko eugene.zelenko@gmail.com wrote:
Hi!
Just re-incarnation of old idea to support 3D image of chemical structures... I played a little bit with Kalzium in KDE 4 today and discovered molecule viewer which render molecules in Chemical Markup Language.
CML (http://cml.sourceforge.net) is open XML-based format so we could allow it on Commons and provide files repository for other projects (such as Kalzium).
There is also Java-based open source viewer JMol (http://jmol.sourceforge.net) including web browser plugin. With JMol we could dramatically enreach chemistry/biochemistry related pages in Wikipedia/Wikibooks/Wikiversity in same way as we support Ogg media files playback now.
See:-
http://en.wikipedia.org/wiki/Wikipedia:Using_Jmol_to_display_molecular_model...
I have been trying off and on over a couple of years to get this on wikipedia. There is a mediawiki extension but it appears to have security issues. It needs someone to address these issues. Personally I would like to see Jmol on wikiversity and that might be a suitable trial before it goes on wikipedia.
More later in this discussion. I must run.
Brian.
Eugene.
-- Brian Salter-Duke b_duke@bigpond.net.au [[User:Bduke]] mainly on en:Wikipedia. Also on fr: Wikipedia, Meta-Wiki and Wikiversity and others. Go Wikimedia Australia Inc, Go!
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l
Commons-l mailing list Commons-l@lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/commons-l