[3dem] PDF with 3D models

Magali Cottevieille mc3077 at columbia.edu
Thu May 22 08:39:06 PDT 2008

Indeed you can do a File > Export Scene with Chimera, hoping that one of 
the formats are recognized by Acrobat 3D.
You bring in an interesting question with these 3D illustrations; they 
would be very useful for a screen display. But what about the paper 
version? Once printed, you loose the benefit of the 3D, but I guess you 
can choose the orientation or display you want to print. Then, the paper 
version maybe still needs to be completed by supplemental material...


> Eduardo
> I see Adobe Acrobat 3D ($699) can be used to create 3D PDF files. 
> Chimera can export VRML scene files that can potentially be imported 
> in Acrobat 3D, so that might be a way to convert map representations. 
> However, I would think that the files will be big (VRML files of map 
> isosurfaces are typically tens of megabytes).
> On May 22, 2008, at 10:18 AM, Eduardo Sanz-Garcia wrote:
>> 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...
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> Bernard Heymann
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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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