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Re: [Jmol-users] Selecting Atoms with the mouse Angel Herráez Fri Feb 03 10:18:26 2012

Hi again Ted 

> I certainly was missing that documentation all together.
> To my mind, the offical documentation was rooted at
> http://jmol.sourceforge.net/
> That did not particulary direct me to the documentation at stolaf.edu that I 
> can recall.
> Perhaps it does and I missed it.

Let's see, Ted. If you still think that route is not clear, please 
advice to impove it. This is what we have:

Jmol main website:  http://jmol.org   
(which leads to http://jmol.sourceforge.net/ )

Top-right menu: "Documentation"
then: "Scripting for Jmol > Scripting Documentation"
"This interactive online documentation is the reference guide for all 
commands ..."


Back to home page, down the page:
"Learn to use Jmol > Manuals and tutorials"
"Finally, there is a documentation section in this web site, for more 
technical details."



Is that not clear? If you did not find it, maybe others won't wither. 
Please suggest.



> There is another issue that I think confronts most new users and that
> is the relationship in Jmol between Java (and the java plugin provided by each
> browser publisher), Jmol Scripting (with it's
> historical relationship with Chime and Rasmol Scripting) and the
> Javascript interface.  One can easily get confused when reading documentation
> and you don't have a grip on which context the documentation is written for.

You might be right. This is not an easy issue. Again, suggestions are 
welcome, as well as collaboration. I feel that Jmol documentation is 
to a lower standard than Jmol features; that's due to lack of 
manpower --or womanpower.  I do what I can in that respect. It's hard 
to match the coding developers efficiency ;-) 

1. "most new users" should not need to worry about Java (other than 
having it installed o their computer). There is nothing involving the 
Java language.

2. The Javascript interface is a way to more easily insert and access 
Jmol applets and pass to it the scripting language.

3. The scripting is th part one must learn by study and testing, and 
where all the power of Jmol is. But still quite a few things can be 
achieved with very little scripting, for basic display. Then you 
quickly grow greedy :) and MUST learn the language!


> I have been spending most of my time in the javascript interface which I think
> is documented at the sourceforge site rather than the stolaf site 

That's right, because it is just so, an interface. To the scripting.


> interface looses most of it's power if I don't understand what's on the 
> otherside
> of it and available in the Jmol Scripting context. It seems like two seperate 
> worlds
> with two pretty seperate sets of documentation,  but to use the full power of 
> Jmol
> I need to know both and I need to not be confused about what is a javascript 
> interface
> method and what is a Jmol scripting function (if I even have that 
> nomenclature correct).

Yes you have. Every Javascipt function (or call) takes a "script" 
argument. That's the link between both "worlds". You have the 
steering wheel and the pedals, but then there is the engine hidden 
somewhere under the trunk :)

I'd guess that different people learn Jmol in different ways.


Ah, there another little mentioned but worthy tool: the Export to Web 
interface included in the Jmol application. It lets you play in Jmol, 
menu and scripting, and then produces a basic webpage for you that 
includes what you have done.



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