[Chimera-users] Antw: Re: Antw: Re: atomic models in pdf

Matthias Barone barone at fmp-berlin.de
Thu Jun 20 12:26:22 PDT 2013

Thats true, AxPyMol only provides a plug in in order to have Pymol
running withing a powerpoint slide. I saw that in a couple of
presentations working quite nicely.

I already tried to export a scene in odj format and then read it with
Photoshop. Im not an expert in these file formats, but when i look at it
in Photoshop, it seems that the odj format safes everything as mesh.
With the effect that electron density and a stick-model become solid
surfaces (see attachment). I will try to find a way to use the html file
and will let you know if I mange to include also mouse gestures in a pdf
Thank you very much for the fast support.

>>> Tom Goddard <goddard at sonic.net> 20.06.13 20.41 Uhr >>>
Hi Matthias,

  I think there are many ways to get Chimera output into 3D PDF if you
are willing to drop $600 on commercial software.  The trouble is that
you have to produce  the 3d model in U3D format and then the U3D can be
embedded in PDF.  Those two conversion steps, going from a Chimera 3d
export format such as X3D to U3D and the U3D to PDF I believe can be
done by many commercial applications.  But I don't know free
applications to do it.  There may well be free applications but it might
take a whole day of digging on the web to find them.  If you do find
them let us know.

  It is easier to find a commercial software conversion route.  For
instance PolyTrans ($395) from Okino Computer Graphics claims to read
X3D and export U3D, and Adobe Acrobat Pro X ($200) can put U3D into PDF



I've never tried this and would definitely worry about whether PolyTrans
or any other software will faithfully handle Chimera's X3D output.

  I think the basic problem is U3D and 3D PDF are used by almost noone. 
The Okino web site gives some idea of the trouble with U3D: "Okino also
has a long history involved with the U3D file format. U3D has quite a
tainted history in the development community. It was derived from the
old Intel IFX 3D gaming toolkit of the 1990's and forced upon developers
as the Macromedia 'Shockwave-3D file format' in 2000. The Shockwave-3D
format was abandoned in 2002 and then it resurfaced in 2004 when Intel
forced it upon Adobe as the 3D file format to use within 3D PDF files
(instead of Adobe using the better X3D file format). With the IFX
toolkit being so buggy, Okino spent much of 2004 through to 2007
debugging the IFX toolkit and creating the main, defacto implementation
of the U3D import/export converters."

  The AxPyMol plug-in you mention does not produce PDF (and is
commercial, $148 academic, or $404 for a lab license, 1 year
subscription).  It embeds 3d PyMol scenes in PowerPoint -- there is no
PDF involved as far as I can tell.  It uses an Active X plug-in (only
available on Windows).


On Jun 20, 2013, at 10:29 AM, Matthias Barone wrote:

Hi Tom and Conrad
Thank you for the fast replies and sorry for not being clear:
Im doing all presentations with the beamer package of latex and hence
search an interactive way to show 3D models of x-ray protein structures
instead of showing pictures.
What Im therefore searching is a way to make a pdf that provides me a 3D
model (incl. mouse gestures like zoom, rotate, clip) with pre-set layout
(ribbon, electron density colours and so on set in chimera). 


>>> Conrad Huang <conrad at cgl.ucsf.edu> 20.06.13 19.16 Uhr >>>
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 b(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. 
> files tend to be large and you need a web browser that supports WebGL
> view them.  The Collada and HTML export are under Chimera menu entry
> File / Export�.  The Collada export is in Chimera daily builds and
> 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
>> but I want to use chimera. You were already discussing a similar
>> in
>> 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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