Robert Hanson wrote the following on 16/07/2010 01:37: > Arie, question for you: I see the two polyhedra models in the PDF file. > But I can't figure out what is going on with the rotation. How is it > that it is working just like jmol, sort of, with the axis in the bottom > left corner spinning around its center, but how then is the model > spinning around a DIFFERENT center? > I guess that this is an Adobe feature > Also, there's some error in that way those polyhedra are rendering -- > faces get lost depending upon the orientation. I wonder if the normals > are wrong. > where is the source of the error? Is it the way Adobe reader implements the interactive stuff, is it the movie15 package, or is there still a problem how Jmol exports idtf (or the idtfconverter)? I haven't seen such problems with molecular models.
> This is going to take some work to get right. > Yes for sure; it would be nice if we could verify the intermediate steps; so I repeat my question: is there an independant idtf/u3d viewer? Strangely enough I do not find anything on the web. Astronomy people use VRML to be embedded as 3D objects in pdf-files: <http://astronomy.swin.edu.au/s2plot/index.php?title=S2PLOT:3dPDF> But the latex/movie15 package is recommended for creating 'professional articles'. Arie > Bob > > On Thu, Jul 15, 2010 at 7:59 AM, Van der Lee <avder...@univ-montp2.fr > <mailto: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} > ********************************* > 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. 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