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<http://www.pymolwiki.org/index.php/Model_Space_and_Camera_Space>.
FYI, there is a bug<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 <joseph.george...@weizmann.ac.il<mailto:joseph.george...@weizmann.ac.il>> 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 ------------------------------------------------------------------------------ _______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net<mailto:PyMOL-users@lists.sourceforge.net>) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net ------------------------------------------------------------ This email message, including any attachments, is for the sole use of the intended recipient(s) and may contain information that is proprietary, confidential, and exempt from disclosure under applicable law. Any unauthorized review, use, disclosure, or distribution is prohibited. If you have received this email in error please notify the sender by return email and delete the original message. Please note, the recipient should check this email and any attachments for the presence of viruses. The organization accepts no liability for any damage caused by any virus transmitted by this email. =================================
------------------------------------------------------------------------------
_______________________________________________ PyMOL-users mailing list (PyMOL-users@lists.sourceforge.net) Info Page: https://lists.sourceforge.net/lists/listinfo/pymol-users Archives: http://www.mail-archive.com/pymol-users@lists.sourceforge.net
