[Chimera-users] atomic models in pdf

Conrad Huang conrad at cgl.ucsf.edu
Thu Jun 20 09:44:57 PDT 2013

Collada format is used by Apple's iBooks Author program to embed 3D 
graphics.  Collada files, with .dae extension, can also be displayed in 
Apple's Preview application.

I don't believe Collada is at all related to PDF, which uses U3D format 
for 3D data.  MeshLab is supposed to read many data formats, including 
Collada, and generate U3D output.  Unfortunately, Chimera Collada output 
is not read properly by MeshLab; triangle per-vertex colors, specified 
as an RGBA data source, seem to be ignored.  Worse, saving U3D output 
(so at least we get the geometric shape) also fails, producing, from 
Chimera's 28MB Collada file, 2 1KB files (no, I don't think it's due to 
compression :-) ).

The bottom line is that I do not have anything new to contribute on the 
PDF front.  Sorry.


On 6/19/2013 9:43 PM, Tom Goddard wrote:
> Hi Matthias,
>    I'm not clear on what your goal is.  You talk about embedding
> molecule models in PDF, in Latex and in HTML.
>    Conrad Huang in our lab added Collada export to Chimera so that
> molecular models could be dropped into some ebook format but I'm not
> sure if that format was PDF or something else.  Have to find out from
> him.  We are also working on displaying 3d views of molecules in a web
> browser using WebGL and Chimera can export an html file for that.  Those
> files tend to be large and you need a web browser that supports WebGL to
> view them.  The Collada and HTML export are under Chimera menu entry
> File / Export….  The Collada export is in Chimera daily builds and HTML
> export is in Chimera 1.8.
> Tom
> On Jun 19, 2013, at 5:41 AM, "Matthias Barone"  wrote:
>> Hi
>> I keep on searching for a solution for embedding atomic models in pdf
>> (by LaTex). In PowerPoint a plugin called AxPyMol does the job nicely,
>> but I want to use chimera. You were already discussing a similar topic
>> in
>> http://plato.cgl.ucsf.edu/pipermail/chimera-users/2008-May/002663.html The
>> question in the topic was whether its possible to incorporate
>> mesh-data (via programs like MeshLab, Photoshop and the movie15
>> package) into .tex files.
>> But Im searching for latex packages to display and manipulate atomc
>> models. Exporting in html could be a way to desplay everything but
>> electron densities (although html doesnt support mouse gestures)
>> sincerly, matthias
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