82.215.1.18 at 17:47, 17 April 2006

2006-04-17T17:47:08Z

NicolasVervelle: Initialization from JmolWiki

2006-03-29T04:57:51Z

Initialization from JmolWiki

New page

= Egon Willighagen =

Together with Miguel the project leaders of the Jmol project.

Also works on other opensource chemistry software, like [http://jchempaint.sf.net/ JChemPaint]
and the [http://cdk.sf.net/ Chemistry Development Kit].

= My Jmol Experience =

Around the summer of 1996 I started working on a website on organic chemistry
([http://www.woc.science.ru.nl/ Dutch Dictionary on Organic Chemistry]) and we needed tools to
add interactivity on the website. I quickly stumbled upon one of the Java applet examples showing
a rotatable model applet that could read XYZ, which was part of one of the earlier Java releases.
I adapted the source code so that it could read PDB files and used this applet on our website.

First, our website was using a file based backend containing the web content. The file format was a
custom one, but when the first XML drafts were published in the net I converted this database
into XML format. I actually found this new application very early because of the work of
Henry Rzepa and Peter Murray-Rust on a chemical application of XML, or the draft actually at
that time. When the final XML specification was released, there application transformed into
Chemical Markup Language.

So, around 1999 (or so, can't remember the exact dates... have to work that out...) I came into
contact with the Jmol and the JChemPaint projects of, respectively, Dan Gezelter and Christoph
Steinbeck, and patched their work to include CML support
[http://www.ijc.com/abstracts/abstract4n4.html IJC article], so that we could more easily
offline maintain our database content, which did include 2D and 3D models of the molecules
in our database. There was my first contact with the virtues of opensource software.
Apperently, both liked my patches and where included in the main source tree.

Later I wrote more patches for both projects, among which an early draft of Rasmol script
interpretation (far from functional compared to the version in Jmol 10) and interpolation for
animations (still to be ported to Jmol 10).

In 2000, Dan, Christoph and I met at Notre Dame University, South Bend, USA, where Dan hosted
a meeting on the future of Jmol and JChemPaint. The Chemistry Development Kit is a direct evolvement
of both projects. In 2003 I worked on making Jmol based on the CDK, e.g. Jmol 9, but Miguel
convincingly showed that the CDK core classes where to heavy for Jmol, so he completely rewrote
Jmol, resulting in the current state-of-art Jmol 10 release.

But, this did not mean the end of Jmol and CDK integration (JmolCdkIntegration).
But that's a whole other story.

Meanwhile, our dictionary website uses the latest Jmol version, and people seem to appreciate
it very much, as we have over 1000 unique visitors each day.

@@ Line 5: / Line 5: @@
 Also works on other opensource chemistry software, like [http://jchempaint.sf.net/ JChemPaint]
 and the [http://cdk.sf.net/ Chemistry Development Kit].
 = My Jmol Experience =

User:EgonWillighagen - Revision history

82.215.1.18 at 17:47, 17 April 2006

NicolasVervelle: Initialization from JmolWiki