Bob,
Yes, no problem, everything is working as you say, including the problem
after mouse rotation within Jmol. Thanks, that simplifies a part of the
processing.
I will see whether I can find some solution for the rotation problem;
Arie
Robert Hanson wrote the following on 16/07/2010 16:13:
> Arie,
>
> I've checked in code for Jmol 12.0.RC26 that:
>
> 1) creates xxxx.idtf.tex along with xxxx.idtf
> 2) gets the orientation correct
> 3) gets the scale correct
> 4) rotates the model around the correct center
>
> The result is that if you have not rotated the model, or if the model
> center is also the screen center, then everything should look right when
> you open the PDF file.
>
> We can't have users optimizing any movie15 coordinates -- say again?
>
> The problem is with rotation. Jmol has two rotation modes -- window and
> "molecular". Generally when you are using the mouse, you are applying
> window-based rotation. But it is also possible to rotate the model
> around its own center, which might not be {0 0 0}. The combination of
> these two modes seems simple and flawless to the Jmol user, but behind
> the scenes it is a VERY tricky business. I remember working quite a long
> time until I figured out how to do that right.
>
> I'm pretty sure the problem is an issue with what I am doing with the
> MOTION business in the IDTF file, but it could be a combination of the
> .idtf.tex and .idtf settings. I don't have any more time today to work
> on this today. If you want to try some things, feel free to make some
> .idtf and .idtf.tex files and then play with the numbers. If you figure
> it out, I will definitely buy you a beer.
>
> Please check out what I have done using
> http://chemapps.stolaf.edu/jmol/docs/examples-11/Jmol.jar
> It's version should be Jmol 12.0.RC26_dev
>
>
> Bob
>
>
>
> On Fri, Jul 16, 2010 at 6:05 AM, Van der Lee <[email protected]
> <mailto:[email protected]>> wrote:
>
> Robert Hanson wrote the following on 16/07/2010 12:44:
>
> OK, I'm in! I have MikTex working and I'm looking at my first
> PDF document. Here was my sequence. Needs refinement, of course!
>
>
> 6. Open doc.pdf
>
>
>
> Now, the rotation and zoom and all will be off. We should be
> able to fix that, though.
>
> What do you mean by: "rotation/zoom" are off? They are not. Use the
> Adobe toolbar and manipulate the object into focus (thus inside the
> defined frame) by a combination of zooming and rotation/translating.
>
> The ideal would be indeed to have the initial view in the pdf-file
> equivalent to the view in Jmol when exporting the idtf-file.
>
> Apart from that your flow sequence is ok. Do not forget that if you
> want to optimize the movie15 coordinates by Adobe Reader itself (use
> the click it option in the latex file, see my previous mail) that
> you need to rerun pdflatex several times in order to get the
> cross-references correct. There is a warning in the log-file if you
> should rerun.
>
> Arie
>
>
>
>
>
>
> On Thu, Jul 15, 2010 at 7:59 AM, Van der Lee
> <[email protected] <mailto:[email protected]>
> <mailto:[email protected]
> <mailto:[email protected]>>> wrote:
>
> Thomas, Bob,
>
> >
> >
> > I'd love to see a short "how to"! :)
> > -Tom
> >
>
>
> Maybe I can satisfy you both at the same time.
>
> Bob's fix worked well (thanks!):
> <http://www.dicoscouts.x10hosting.com/perez.pdf>
>
> For those of you who never opened an interactive pdf before some
> guidelines:
> 1) click on the structure and keep the left button pressed while
> rotating the structure - as you would do in Jmol
> 2) similarly use the mouse wheel to zoom/dezoom
> 3) right click for more options, including the appearance of
> a task bar
>
> That's all.
>
> As far as I know you can only use the Adobe Reader starting
> from version
> 7 and not pdf readers. However, I prefer the latest version
> 9, because
> in at least version 8 there is a dotted frame appearing
> around the
> structure as soon as you click the 3D object. In AR9 this
> frame is
> absent, but there is a default 'compass' in the lower left
> corner but
> this one can be de-activated in the Reader's options (3D
> content tab)
>
> If your 3D object is really big (ED map, macromolecule maybe)
> then you
> need computer power in order to see your object in the reader. My
> computer has 3Mb ram and a 3.3GHz processor. You may be
> disappointed if
> you connect your small notebook (let's say 1.6GHz and 1Mb
> RAM) to the
> congress beamer ... Although in the latter case you can
> decide to set
> the image frequency to a lower value in the Reader's 3D
> options and/or
> to change the optimisation method for small frequency to
> 'Abandon'. And
> it is a good idea to preload the pdf in the Reader before
> doing the
> actual presentation.
>
> How can one create such a pdf? You can find bits and pieces
> on the Web,
> including those in the Jmol wiki. In short it is this:
>
> 1)create your structure in Jmol and write an IDTF file
> write IDTF "file.idtf"
> 2)convert the idtf file to u3d format with the idtfconverter,
> see also
> here:
> <http://wiki.jmol.org/index.php/File_formats/3D_Objects#U3D>
> 3)pdflatex a file like the following minimal example
> *************************************
> \documentclass[12pt,a4paper]{article}
> \usepackage{hyperref}
> \usepackage[3D]{movie15}
>
> \pagestyle{empty}
>
> \begin{document}
>
> \begin{center}
> \includemovie[
> label=een,
> autoplay,
> repeat=1,
> toolbar=true,
> 3Droo=33.34789768949952,
> 3Dcoo=0.000000257883272070 -0.000000283616543584
> -0.000000327838080239,
> 3Dc2c=-0.7544490694999695 -0.5638955235481262
> 0.33589935302734375,
> 3Droll=-18.778433745507403,
> 3Dbg=.66 1. 0.83,
> 3Dlights=Headlamp,
> inline=true,
> ]{0.9\textwidth}{0.9\textwidth}{een.u3d}
> % \\
> %\movieref[3Dcalculate]{een}{Click here!}
> \end{center}
> \end{document}
> *********************************
> 4) decomment in a first run the \movieref line. You will have the
> possibility to better center the object and by clicking on
> 'click here!'
> AR calculates you a new set of coordinates that may replace
> by copy and
> paste the old set. The bigger the object the longer AR takes to
> calculate the set of coordinates. Be patient, this may be
> long and not
> feasable on a notebook. By the way, if your initial set of
> coordinates
> is totally wrong, then you may not see your object at all
> after the
> initial pdflatex runs. You need to zoom or dezoom and/or
> translate to
> get the object into your visible frame.
> 5) as soon as you have a nice set of coordinates you may
> comment again
> the movieref line and set toolbar to false.
>
> This is it: yes it is a bit cumbersome, but it is worthwhile
> if you want
> to have your structure/molecules as 3D objects in your pdf
> presentation.
> The alternative is of course to open Jmol next to your
> presentation. The
> advantage is that you have all the options of Jmol available,
> which you
> do not have in AR - the only thing you can do there is
> rotating/translating/zooming. But if your presentation is
> only 20 or 30
> minutes, I prefer to do it without 'break', thus without
> opening another
> application. Of course this is a matter of taste.
>
> Sorry Tom, it was not that short.
>
> best wishes, Arie
>
>
>
>
> --
>
>
> ***************************************************************************
> A. van der Lee
> Institut Européen des Membranes
> CNRS - UMR 5635
> Université de Montpellier II - Case Courrier 047
> Place E. Bataillon
> 34095 MONTPELLIER Cedex 5 - FRANCE
>
> Tel : 33 (0) 4 67 14 91 35
> Fax : 33 (0) 4 67 14 91 19
>
> Website X-ray scattering facility ICG/IEM:
> http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html
>
>
> ****************************************************************************
>
>
>
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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
>
>
>
> --
>
> ***************************************************************************
> A. van der Lee
> Institut Européen des Membranes
> CNRS - UMR 5635
> Université de Montpellier II - Case Courrier 047
> Place E. Bataillon
> 34095 MONTPELLIER Cedex 5 - FRANCE
>
> Tel : 33 (0) 4 67 14 91 35
> Fax : 33 (0) 4 67 14 91 19
>
> Website X-ray scattering facility ICG/IEM:
> http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html
>
> ****************************************************************************
>
>
>
>
> --
> 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
--
***************************************************************************
A. van der Lee
Institut Européen des Membranes
CNRS - UMR 5635
Université de Montpellier II - Case Courrier 047
Place E. Bataillon
34095 MONTPELLIER Cedex 5 - FRANCE
Tel : 33 (0) 4 67 14 91 35
Fax : 33 (0) 4 67 14 91 19
Website X-ray scattering facility ICG/IEM:
http://www.iemm.univ-montp2.fr/xrayweb/main_uk.html
****************************************************************************
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