Re: [Jmol-users] jmol related workflow question

[Egon W. <e.w...@sc...>]

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On Friday 27 August 2004 19:20, Rajarshi Guha wrote:
> Has anybody faced this type of situation before? I would rathr not have
> students draw molecules in one package, move the files aorund, write job
> scripts and then get output and view that - too much scope for mistakes.
> If this could be bundled in a webpage which takes the 3D coordinates,
> writes a job script, takes the output and displays it Jmol that would be
> great.

Hens Borkent might likely respond himself too, but I'll point to his page=20
anyway:

http://www.cmbi.kun.nl/wetche/organic/mopjob.html

You'll see a menu on that page with, for a number of chemical problems, two=
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applications, one older, and one implemented with Jmol...

The approach they use is this:

the start a Jmol applet and let students select a hydrogen, and then, with =
a=20
drop down box, the students can select groups which they want to have repla=
ce=20
the selected hydrogen, and then after pressing the replace button, the page=
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gets reloaded with the new molecule... A basic way of building molecules...=
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(internally it's using Z-matrices to build the molecule in 3D)

When the student is happy with there 3D creature, the can let MOPAC deal wi=
th=20
it... Browse around and see if it is enough for your purposes too...

Egon

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e.w...@sc...
PhD on Molecular Representation in Chemometrics
Radboud University, Nijmegen
http://www.cac.science.ru.nl/people/egonw/
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