Re: [Jmol-users] Making movies

[A. H. <ang...@ua...>]

Hello Arjan

> My question: 
> I'd like to make a movie of an esterification where molecules/atoms of the reactants move to 
> form the ester. I've been searching the net now for 2 days, but I cannot find any documentation 
> on this. Maybe I'm searching in the wrong place, so I've turned to you. I downloaded a xyz-file 
> and included it in this message, to give you an idea of my intentions. 

> Is there a program to make these files or do I have to start understanding the script (yes, I know, 
> that's probably a good idea anyway:-]) 

Yes, the problem is building the multi-model file for your reaction, similar to the one you 
downloaded. But that's not a Jmol task. Jmol will just display-animate the model once you 
have it built. There is little you can learn from scripting, apart from the way to play the 
animation.
I do not know of a program that you can use to build the model.


In fact, the thing MAY be done using Jmol scripting, as it can move atoms around, but that's 
not trivial at all. I'd rather look for an external way to build the multi-model file.

There are a few websites that have animated mechanisms of reaction. Maybe you can find 
yours already built there.

Please check out sites at
http://wiki.jmol.org/index.php/Websites_Using_Jmol

I particularly suggest  ChemTube3D, by Nick Greeves. For example:
http://www.chemtube3d.com/Nucleophilic%20substitution%20at%20the%20carbonyl%20gro
up%20-%20Acid-catalysed%20ester%20hydrolysis%20and%20transesterification.html

Once you've got your model, you may come back to this list if you need help with playing 
the animation. I (we) will be glad to help you.

Good luck!