Way cool!
Couple of questions or comments.
1. I know nothing about these file formats. I assume there is a good reason
that the U3D format can't be written directely? Seems odd that you have to go
through some intermediary format.
2. I've got no experience with server side programming. Seems like some clever
person could create a web page that allows one to load a molecule into Jmol,
display it as they want, write this xxx.idtf file, and send it to some server
side script that does the rest and returns the pdf file. Perhaps using
something like this
http://www.scribtex.com/
***********************************************
Jeff Hansen
Department of Chemistry and Biochemistry
DePauw University
602 S. College Ave.
Greencastle, IN 46135
jhan...@depauw.edu
***********************************************
On Jul 17, 2010, at 4:36 PM, Robert Hanson 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
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