That would be a Jmol bug. One issue is that the idtfconverter doesn't give
any clue as to what these errors are.
Please send the IDTF and IDTF.TEX files to me.
Bob
On Tue, Jul 20, 2010 at 1:13 PM, Thomas Stout <thomasjst...@gmail.com>wrote:
>
>
> Well, I'm stumped. I've followed all the terrific "recipes" from Bob and
> Angel and I keep hitting a brick wall. Everytime I try to run
> IDTFConverter, I get the following:
>
> C:\temp> u3d 1crn
> C:\temp> c:\idtf\IDTFConverter.exe -input 1crn.idtf -output 1crn.u3d
> Exit code = 80000003
>
> (it happens instantly and no output file is created)
>
> I've googled that message and it simply means that a breakpoint was
> encountered. Has anyone else come across this (and resolved it)?!
>
> I'm attempting this on a high-end PC running WinXP, SP2 (fast, lots of RAM,
> etc).
>
> I'm very eager to get this working, so it's a bit frustrating......
> -Tom
>
>
>
>
> On Sat, Jul 17, 2010 at 1:36 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
>>
>>
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>
>
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--
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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