Re: [PyMOL] How does PyMOL create .obj file?

Hi Joe -

The coordinate system in the .obj file is in camera space, where (0,0,0) is the center of the viewport, positive x to the right, positive y up, and positive z out of the screen toward the viewer.  If you want to correlate them, you would need to transform the model coordinates using the view matrix or, probably more easily, set the view to coincide with model space, as specified under "Space and File saving" here<." rel="nofollow">http://www.pymolwiki.org/index.php/Model_Space_and_Camera_Space>.

FYI, there is a bug<" rel="nofollow">https://sourceforge.net/p/pymol/bugs/170/> in .obj output of spheres, which are output as a single triangle face with identical coordinates for all three points.  Needless to say, you can't see them, unless you zoom in really close.  Also, cylinders and cones are not yet implemented in .obj output, so, basically the only representation fully supported is surfaces, which are made entirely of triangle meshes.

Hope that helps.

Cheers,
Jared

--
Jared Sampson
Xiangpeng Kong Lab
NYU Langone Medical Center
http://kong.med.nyu.edu/




On Aug 15, 2015, at 1:34 PM, Joseph Georgeson <jos...@we...<mailto:jos...@we...>> wrote:

Hi all,

I'm trying to correlate an .obj file created in PyMOL to the actual molecular coordinates of a protein from the .pdb file. Is this possible? Does anyone know how PyMOL creates the .obj file?

Thanks,
JoeG
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