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
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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
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. Conrad 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 _______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu <mailto:Chimera-users@cgl.ucsf.edu> http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
_______________________________________________ Chimera-users mailing list Chimera-users@cgl.ucsf.edu http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users
participants (3)
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Conrad Huang -
Matthias Barone -
Tom Goddard