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Re: [Jmol-users] idtf output for polyhedral structures
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From: Robert H. <ha...@st...> - 2010-07-16 15:55:38
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OK. Just for reference, here are the issues:
-- In Jmol the center of window (mouse) rotation is not necessarily the
point {0 0 0} nor is it necessarily the center of the model.
-- In Jmol the center of rotation may not be positioned directly in front of
the user, at the window center. It may be offset ("translated") in the XY
pixel plane. (CTRL-ALT-drag)
-- Zooming in Jmol is based on the center of rotation, wherever it is in the
XY window plane, not the window center.
-- The perspective in Jmol should be the same as other programs (starting
with Jmol 11).
This is a different model than the one used in VRML or U3D or the general
CAD business, I think. In those cases, you don't generally hold the object
at arms' length and rotate it with your wrist, instead you walk around the
model. Or, to put it another way, in Jmol the mouse is used to rotate the
model, not change the camera position, and zoom is like looking through a
telescope, not moving into the model (unless you are in navigation mode.) At
least that's what I've gathered with my meager experience with these
programs.
The point is that while we should be able to get the opening scene right, it
will be a good trick to get the mouse action to be the expected action. U3D
is pretty general, so I suspect there is a way to do it -- it just may take
some careful experimentation.
Still, I think this is a good start.
Bob
On Fri, Jul 16, 2010 at 10:06 AM, Van der Lee <avd...@un...>wrote:
> 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 <avd...@un...<mailto:
>> avd...@un...>> 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
>> <avd...@un... <mailto:avd...@un...>
>> <mailto:avd...@un...
>> <mailto:avd...@un...>>> 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
>
> ****************************************************************************
>
--
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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