Hi Francois, That information is in the view matrix you get from get_view. The first nine numbers are the rotation matrix R. The next three numbers are the camera position c, followed by the three numbers denoting origin of rotation o. Then to transform your protein coordinates, as in the PDB, to match up with your output from pymol, for each coordinate x, you do:
y = R %*% (x - o) + c where %*% denotes matrix multiplication. Hope it helps, Tsjerk On Fri, Apr 8, 2011 at 11:02 AM, Francois Berenger <beren...@riken.jp> wrote: > Jason Vertrees wrote: >> Hi Francios, >> >> Someone recently asked about this and the answer was that this should >> be a setting, but isn't currently available. If I have time, I'll try >> to sneak this in the upcoming PyMOL v1.4 release. > > Is there a workaround for the moment? > > For example, asking Pymol what is the current rotation > and translation the model being displayed has undergone > compared to the initial PDB that was read in? > > With such a possibility, it would allow one to > know how to rigid body transform the input PDB > in order to have it aligned with the surface Pymol is > writing to a .obj file. > > Thanks a lot, > Francois. > >> Cheers, >> >> -- Jason >> >> On Fri, Feb 25, 2011 at 3:05 AM, Francois Berenger <beren...@riken.jp> wrote: >>> Hello, >>> >>> Is it possible to save the Connolly surface >>> computed by Pymol without any rotation and translation >>> added compared to the PDB from which the atom coordinates were read? >>> >>> I looked at the .obj file output and find there was some centering >>> done and also some rotation added. >>> >>> Thanks a lot, >>> F. >>> >>> ------------------------------------------------------------------------------ >>> Free Software Download: Index, Search & Analyze Logs and other IT data in >>> Real-Time with Splunk. Collect, index and harness all the fast moving IT >>> data >>> generated by your applications, servers and devices whether physical, >>> virtual >>> or in the cloud. Deliver compliance at lower cost and gain new business >>> insights. http://p.sf.net/sfu/splunk-dev2dev >>> _______________________________________________ >>> 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 >>> >> >> >> > > > ------------------------------------------------------------------------------ > Xperia(TM) PLAY > It's a major breakthrough. An authentic gaming > smartphone on the nation's most reliable network. > And it wants your games. > http://p.sf.net/sfu/verizon-sfdev > _______________________________________________ > 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 > -- Tsjerk A. Wassenaar, Ph.D. post-doctoral researcher Molecular Dynamics Group * Groningen Institute for Biomolecular Research and Biotechnology * Zernike Institute for Advanced Materials University of Groningen The Netherlands ------------------------------------------------------------------------------ Xperia(TM) PLAY It's a major breakthrough. An authentic gaming smartphone on the nation's most reliable network. And it wants your games. http://p.sf.net/sfu/verizon-sfdev _______________________________________________ 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
