On Thu, Jul 15, 2010 at 7:59 AM, Van der Lee <avder...@univ-montp2.fr>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}
> *********************************
>
AH-HAH! That's what I've been looking for. How do these values for 3D
parameters relate to our perspective in Jmol? We can have Jmol write this
file if you can explain it.
> 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.
>
OK, we can do this automatically. Will take some experimentation. Can you
help, Arie? We need to see exactly what the relationship is between the
numbers there and (perhaps)
show orientation
or
show rotation
I would recommend starting by using simple orientation changes such as
reset
rotate x 90
rotate y 90
rotate z 90
(one of those, not all!)
and seeing what you have to use for parameters. I see this description:
3Daac=<angle> This option sets the aperture angle of the camera,
measured in degrees. Fixed point real numbers
between 0 and 180 are admissible. A sensible value
of 30 is pre-set by default. Larger values can be
used to achieve wide-angle or fish-eye effects.
3Dc2c=<x> <y> <z> Direction vector C2C of arbitrary length,
originating in the centre of orbit and pointing
to the virtual camera; cf. option `3Dcoo' for the
number format of <x> <y> <z>.
3Dcoo=<x> <y> <z> Positional vector COO of the centre of orbit.
Only fixed point numbers in the range from
-999999999999999999.999999999999999999 to
+999999999999999999.999999999999999999 are
allowed.
3Droll=<roll> Prescribes an initial camera roll around the
optical axis (in clockwise direction, if <roll>
is greater than zero); measured in degrees.
3Droo=<r> Radius of orbit ROO of the virtual camera; cf.
at http://www.ctan.org/tex-archive/macros/latex/contrib/movie15/, so this
should not be too difficult to figure out.
3Daac will probably be fixed.
3Dc2c should relate directly to the mapping of {0 0 1} to screen
coordinates.
3Dcoo should be the center of rotation
3Droll can be calculated from the transformation matrix, I think. This can
be gotten from
print quaternion(script("show rotation"))%-9
3Droo should be easily related to zoom
> 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.
>
>
Let's get this into JMol 12.0. Now!
Bob
> 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
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