I've uploaded the files for 1crn default view at
http://stolaf.edu/people/hansonr/jmol/test/pdf so you can see where I am at.
Bob
On Fri, Jul 16, 2010 at 9:13 AM, Robert Hanson <[email protected]> wrote:
> 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]>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]>> 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
>
--
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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