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Topic: ChemTube3D - Interactive 3D Organic Reaction Mechanisms  (Read 17254 times)

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Offline ng

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ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« on: May 15, 2008, 08:54:52 AM »
I would like to draw to your attention ChemTube3D http://www.chemtube3d.com
This is a web based educational resource which is under active development.

It was developed using Jmol to depict interactive 3D animations for some of the most important organic reactions covered during an undergraduate degree with supporting information on reactivity and spectroscopy. Each intermediate and each mechanistic step is presented in turn, for careful consideration in 3D, providing additional insight.

It is intended to supplement existing textbooks and lectures and I use it regularly projected. Direct links to particular reactions can be added to VLEs or students can browse for themselves.

This is part of an  an ongoing Development project supported by the
Higher Education Academy Physical Sciences centre.

If you have any suggestions for additional content that would assist our teaching, please let me know. Jmol is a remarkable free tool for displaying chemical information and works with a wide range of formats http://jmol.sourceforge.net/

Offline Mitch

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #1 on: May 15, 2008, 04:59:30 PM »
The E2 elimination example page crashed firefox and made me do a computer restart. This is why I hate jmol and will never ever use it or advocate it.
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Offline ng

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #2 on: May 15, 2008, 05:47:03 PM »
That's a bit disturbing, Firefox works fine for me on Mac OS X and Windows XP.

Can you give me the precise URL, OS, version of FF, and Java version that causes the crash?

If I can replicate it, I can fix it.

Offline Mitch

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #3 on: May 15, 2008, 06:02:50 PM »
It was in this page: http://www.chemtube3d.com/Elimination%20-%20E2.html
Windows XP, firefox 2.0.0.14. Java(TM) 6 update 2, and J2SE runtime environment 5.0 update 6.

I'm about to try the url again, here I go.
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2. Don't confuse thermodynamic stability with chemical reactivity.
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Offline Mitch

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #4 on: May 15, 2008, 06:05:32 PM »
No crash, but now I get "java.security.AccessControlException: access denied(java.io.FilePer" the rest of it is off the black box window.
Most Common Suggestions I Make on the Forums.
1. Start by writing a balanced chemical equation.
2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

Offline ng

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #5 on: May 15, 2008, 06:18:19 PM »
I have seen that error message but that page is working for me. There has been a recent change to Firefox (Win and linux) which makes it very sensitive to "security" issues.

If you persevere by clicking on the reaction scheme or on other reaction pages you should find the applet works well. It did for me just now Win XP/FF and IE and Mac/FF and Safari



Offline Mitch

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #6 on: May 15, 2008, 06:47:07 PM »
Doesn't work with my ie either. I get same message. ie version is 7.05730.11
Most Common Suggestions I Make on the Forums.
1. Start by writing a balanced chemical equation.
2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

Offline ng

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #7 on: May 15, 2008, 07:00:46 PM »
Did you try clicking on the reaction mechanism to load intermediates or 3D curly arrows?

That works for me XP/IE 7 (don't know where to find the version!)

Or even try the less elegant URL http://138.253.125.24/~ng/external/ The numerical IP address avoids the recent Java security issue.


Perhaps others could post their experiences, good and bad?

Offline Mitch

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Re: ChemTube3D - Interactive 3D Organic Reaction Mechanisms
« Reply #8 on: May 15, 2008, 08:56:51 PM »
It seems to work on my laptop just fine; windows vista, firefox. Jave, with its sometimes it works and sometimes it doesn't workings makes me avoid it like the plague.
Most Common Suggestions I Make on the Forums.
1. Start by writing a balanced chemical equation.
2. Don't confuse thermodynamic stability with chemical reactivity.
3. Forum Supports LaTex

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