Hi all, PyMOL allows for both camera and object coordinate changes. When you use the mouse to move stuff around, that's the camera moving*--just like the 'turn' command. When you use "rotate", object dragging or some of the other matrix transformation commands (fit, super, align, matrix_copy, update, etc) you are affecting the coordinates of the objects themselves.
Try the following ton convince yourself: # get a protein fetch 1oky, async=0 # the original view matrix get_view # move the camera & get view turn x, 90 get_view # rotate 1oky & get view rotate x, 90, 1oky get_view Compare the values after turning vs rotating. This brings up another point, for large molecular assemblies, it's much faster internally to use 'turn' rather than 'rotate'. 'Turn' is simply a matrix multiplication, the other is that and storing the new coordinates back into the object. Cheers, -- Jason * -- you can move objects themselves with the mouse, but only in editing or dragging mode On Wed, May 12, 2010 at 4:27 AM, Tsjerk Wassenaar <tsje...@gmail.com> wrote: > Hi Robert, > > PyMOL>help rotate > > DESCRIPTION > > "rotate" can be used to rotate the atomic coordinates of a > molecular object. Behavior differs depending on whether or not the > "object" parameter is specified. > > <snip> > > So much for rotate. The help for turn is misleading: > > PyMOL>help turn > > DESCRIPTION > > "turn" rotates the camera about one of the three primary axes, > centered at the origin. > > <snip> > > It does not turn the camera, actually. It changes the orientation of > the scene with respect to the camera. The effect is the same, and you > can interconvert. That is the basis for the povray macros I wrote some > while ago to combine things in object space with those in the pymol > camera space in the exported scene. > > Cheers, > > Tsjerk > > On Wed, May 12, 2010 at 9:21 AM, Robert Fenwick > <robert.fenw...@irbbarcelona.org> wrote: >> >> What is the difference between the turn and the rotate commands? >> On 12 May 2010, at 06:21, Tsjerk Wassenaar wrote: >> >> Hi Mike, Tom, >> >> If I'm not mistaken, it is always the camera that is moving when you rotate >> >> a molecule. >> >> Unfortunately I have to inform you that you are mistaken... In Pymol >> the camera is always fixed. That also means that it is not possible to >> have the camera fly through the protein. >> >> But there isn't really any difference with the protein flying around >> the camera. You can interconvert object oriented view and camera >> oriented view. Have a look at http://pymolwiki.org/index.php/Get_view, >> http://pymolwiki.org/index.php/Set_view and >> http://pymolwiki.org/index.php/Scene for starters. >> >> Hope it helps, >> >> Tsjerk >> >> >> Hello everyone, >> >> I am trying to do something that seems a little uncommon. I wish to have a >> >> moveable camera. So instead of rotating/translating the protein/molecule/DNA >> >> I move the camera point/location and the vector that the camera points in. I >> >> wish to be able to move into the molecule and view binding pockets from the >> >> perspective of the molecule. I have tried a few web searches on this and >> >> thought I would ask everyone here if they have heard of something similar? >> >> I am currently trying to find some 3d modelling software that will load a >> >> .PDB file so that I can export it to a game engine (Unreal development kit) >> >> as a back up method if all else fails. >> >> Thanks for your time, >> >> Tom >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> >> 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 >> >> >> >> -- >> >> Michael Zimmermann >> >> Ph.D. student in Bioinformatics and Computational Biology >> >> Department of Biochemistry, Biophysics and Molecular Biology >> >> Iowa State University >> >> ------------------------------------------------------------------------------ >> >> >> _______________________________________________ >> >> 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 >> University of Groningen >> The Netherlands >> >> ------------------------------------------------------------------------------ >> >> _______________________________________________ >> 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 >> >> R. Bryn Fenwick >> robert.fenw...@irbbarcelona.org >> Post-doctoral fellow >> Chemistry and Molecular Pharmacology Programme >> Institute for Research in Biomedicine (IRB Barcelona) >> Parc Científic de Barcelona >> Baldiri Reixac 10, 08028 Barcelona, SPAIN >> Tel. (+34) 9340 20460 >> >> >> > > > > -- > Tsjerk A. Wassenaar, Ph.D. > > post-doctoral researcher > Molecular Dynamics Group > Groningen Institute for Biomolecular Research and Biotechnology > University of Groningen > The Netherlands > > ------------------------------------------------------------------------------ > > _______________________________________________ > 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 > -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ _______________________________________________ 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
