Hi Spencer, Thank you very much for the script! I'll test it out right away.
Best, JJ On 1 Sep 2016, at 10:31 AM, Spencer Bliven <spencer.bli...@gmail.com<mailto:spencer.bli...@gmail.com>> wrote: Jingjie, I've used a script for calculating the principal components (https://github.com/sbliven/principal_axes). The computeprincipalaxes function returns the axes. With a bit of linear algebra you should be able to use that to get a transformation matrix to apply to the coordinates. This can be passed to Transform_selection<http://www.pymolwiki.org/index.php/Transform_selection>. Another approach might be to use the orient command, and then use get_view to extract the view matrix. Applying the inverse of this to the coordinates should orient them along the XY axes. -Spencer On Thu, Sep 1, 2016 at 3:46 PM, #YEO JINGJIE# <jy...@e.ntu.edu.sg<mailto:jy...@e.ntu.edu.sg>> wrote: Hi Jared, Thank you very much for your information. However, it seems that orient only changes the viewpoint, may I know whether it would possible to change the coordinates accordingly and save it into a pdb? Best Regards, Jingjie On 31 Aug 2016, at 10:16 PM, Sampson, Jared M. <jms2...@cumc.columbia.edu<mailto:jms2...@cumc.columbia.edu>> wrote: Hi Jingjie - The `orient<http://www.pymolwiki.org/index.php/Orient>` command does this, although you can't specify which axis. However, when combined with `turn<http://www.pymolwiki.org/index.php/Turn>` or `rotate<http://www.pymolwiki.org/index.php/Rotate>`, you can get the molecule aligned in whichever orientation you prefer. E.g: orient myprotein turn x, 90 turn y, -90 Hope that helps. Cheers, Jared On Aug 31, 2016, at 6:10 PM, #YEO JINGJIE# <jy...@e.ntu.edu.sg<mailto:jy...@e.ntu.edu.sg>> wrote: Dear Users, May I know whether there are any methods in pymol to rotate a protein such that it's longest principal axis is in a particular direction, for instance aligned to the x-axis? Best Regards, Jingjie **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University. ------------------------------------------------------------------------------ _______________________________________________ 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 **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University. ------------------------------------------------------------------------------ _______________________________________________ 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 **Disclaimer** The sender of this email does not represent Nanyang Technological University and this email does not express the views or opinions of the University.
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