[3dem] PDF with 3D models

Leonardo Trabuco ltrabuco at ks.uiuc.edu
Thu May 22 10:10:37 PDT 2008


VMD provides support for Acrobat3D. You may wanna check this out:


On Thu, May 22, 2008 at 11:27:43AM -0400, Magali Cottevieille wrote:
> Hi Eduardo,
> I didn't know this new feature of Acrobat, it's impressive. I wish it 
> could be applied to scientific publications in biology. I don't think 
> there is any viewer able to generate such figures, since Adobe is 
> selling its own 3D pdf generator:
> http://www.adobe.com/products/acrobat3d/.
> So you will probably have to pay  US$699 for the licence.
> Another issue is even if you buy it, you have no insurance that you can 
> use in input your usual material. Adobe says that the normal CAD formats 
> are recognized... Maybe you could try to download the trial version...
> Magali
> >Today, I was reading a correspondence in Nature 
> >(http://www.nature.com/nature/journal/v453/n7194/full/453450d.html) 
> >that talks about the PDF capabilities of displaying 3D models. It is 
> >possible to rotate, and zoom in and out the 3D model from inside the 
> >PDF viewer (you can see some examples here: 
> >http://www.3dhh.de/3d-PDF/index-en.htm).
> >I was wondering if there is any cryo-EM package that allows to save 3D 
> >models in PDF format. I don't know if this is even possible. Maybe too 
> >many vertex are necessary to represent accurately a cryo-EM 
> >isosurface, and the final PDF file would be too big. How about atomic 
> >coordinate models?
> >I would like to open a discussion about the usefulness of this concept 
> >in our field. Would you like to read a paper and be able to rotate, 
> >zoom in/out the figures (I don't even know if there is possible to 
> >include several 3D model in the same PDF and along with normal test). 
> >I know that cryo-EM models and PDB files are always included as a 
> >supplemental material, but sometimes it is difficult to display the 
> >same area, you lose coloring, labels, etc. Superfluous, necessary, 
> >imposible, the future? The end of stereographic images? More work for 
> >authors?
> >Your comments...
> >_______________________________________________
> >3dem mailing list
> >3dem at ncmir.ucsd.edu
> >https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem
> -- 
> Magali Cottevieille, Ph.D.
> Howard Hughes Medical Institute,
> Department of Biochemistry and Molecular Biophysics,
> 630 W 168th St, P&S Black Building 2-221
> New York, NY 10032 
> Ph:  (+1) 212-305-9521
> Fax: (+1) 212-305-9500
> Email: mc3077 at columbia.edu
>       magali.cottevieille at gmail.com
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Leonardo Trabuco, Ph.D. student
Theoretical and Computational Biophysics Group
University of Illinois at Urbana-Champaign

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