Oh-- forgot to mention -- Jmol 12.0.RC26_dev is available at
http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.jar
On Sat, Jul 17, 2010 at 3:36 PM, Robert Hanson <hans...@stolaf.edu> wrote:
> OK. Got it! Whew! My work is about done on this.
>
> Arie, now I REALLY owe you a beer.
>
> Fellow Jmol users - check this out. You can now export models from Jmol and
> have VERY NICE reproductions in a PDF file. I've uploaded some test files
> into http://chemapps.stolaf.edu/jmol/docs/examples-11/pdf
>
>
> The workflow looks like this:
>
> JMOL: write xxx.idtf
>
> (This process creates TWO files -- xxxx.idtf and xxxx.idtf.tex. The idtf is
> the "intermediate" file format that is needed in the next step to create a
> U3D file, which is what goes into the PDF as a 3D "movie"; the idtf.tex
> files contains the Jmol state (in a Tex comment) and a bit of TeX code that
> sets the zoom correctly (the part I couldn't figure out on my own, Arie) and
> can be used to create a sample PDF file using a program such as MikTeX.
> There are parameters in there that can be tweaked such as the zoom rotation,
> and such.)
>
> I recommend also along with this,
>
> write xxx.png
>
> Just so you have the image and associated state if you want that.
>
>
> SHELL: use idtfConverter to create a U3D file from IDTF.
>
> (I might note that Jmol is VERY EFFICIENT in its use of nodes in creating
> these files. If you have ever first created a VRML file and then had another
> program create the U3D from that, you will have noticed that a small enzyme
> could be 15 Mb of U3D file. Jmol caches all objects and only creates new
> ones when it is absolutely necessary.)
>
> MikTeX/TeXworks or other pdf-creating software: Open and run the idtf.tex
> file
>
> That's it! In many cases you will get a nearly EXACT 3D model relative to
> what you see in Jmol.
>
> I was creating PDF documents in less that 10 seconds from the "write"
> command once I got it figured out.
>
> There are several CAVEATS:
>
> 1) If you move the model rotation center away from screen center, as with
> CTRL-ALT-drag, you are going to get a very good, very close, but not quite
> perfect reproduction of the model in VRML or U3D. That moving of the center
> of perspective is not supported in those virtual reality packages, as far as
> I can tell. I guess no one has ever considered it.
>
> 2) I can't get lighting to work. When I try, I get a light that moves with
> the model. So if someone knows how to do that, speak up.
>
> 3) I can't see how to set the perspective to ORTHOGRAPHIC. If you have used
> Jmol you may not even have noticed, but if there is a crystal structure that
> structure is being rendered with perspectiveDepth turned off - otherwise the
> unit cells are very odd. There is a right-mouse-button option to go into
> that mode, but I don't see how to require that up front. Please let me know
> if you know how to do that.
>
> 4) Don't expect the operation of the PDF mouse interface to be like Jmol.
> In my hands, at least, it is quite difficult to control. I don't get the
> mouse motion model at all, actually, and I particularly don't like the fact
> that I can completely lose the rotation center somehow.
>
>
> But, if you can live with that, this is quite cool.
>
> (more notes below...)
>
> 2010/7/16 Angel Herráez <angel.herr...@uah.es>
>
>>
>> > needed for big objects, and also what you can do to render it more
>> > fastly.
>>
>> > - see one of my earlier mails, notably on the computer power
>> Well, everytime we have discussed this VRML / X3D / IDTF / U3D / PDF
>> business, I get rather excited about the possibility --and involved--, but
>> it the end I think this is not at all comparable to what you get by just
>> setting a webpage with JmolApplet -- much faster, smoother and smaller.
>>
>>
> true, but can you do that on an iPhone? [not that iPhones can support U3D
> movies within PDF -- or can they? If you have an iPhone or iPad, do check
> out http://chemapps.stolaf.edu/jmol/docs/examples-11/pdf/test.pdf I'm
> betting the chances of that are way higher than Apple coming around to
> seeing the value of Java]
>
>
>
>
>> It's just a way to reach a separate community. Nothing like the real
>> stuff!!
>>
>> I'm also eager to have a way to easily and cheaply (that is, zero cost
>> in software) produce a model embedded in a pdf that has text content too,
>> not just the model.
>>
>>
> The TeX-aware folks will go nuts with this; the rest of us have to tag
> along. If you Adobe Pro, then you can add text to a PDF document that has
> already been made and you can copy and paste objects ("movies" like this??)
> from one document to another.
>
>
>
> Bob
>
>
> --
> Robert M. Hanson
> Professor of Chemistry
> St. Olaf College
> 1520 St. Olaf Ave.
> Northfield, MN 55057
> http://www.stolaf.edu/people/hansonr
> phone: 507-786-3107
>
>
> If nature does not answer first what we want,
> it is better to take what answer we get.
>
> -- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
>
--
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107
If nature does not answer first what we want,
it is better to take what answer we get.
-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900
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