Hello Warren, Thank you very much for your advice.
I guess I was not being very clear. what i meant was that i would also like to save the coordinates of this reoriented polymer. Let me be clear: I have a polymer aligned along y-axis. I change some of the dihedral angles. As a result, the chain is pointing in some arbitrary direction. So, I want to re-orient the polymer along the y-axis and then save the coordinates of this reoriented polymer. I used the command "orient" from the installed pymol on my system (version 1.0r2). But when I try to save the polymer, it still saves the same coordinates as the one before reorientation. Please let me know if something can be done ? Thank you, Vivek On Tue, Jun 2, 2009 at 8:50 PM, Warren DeLano <war...@delsci.com> wrote: > You can save a copy of the original and then superimpose the copy back onto > it > > # using "fab" command from the latest 1.2 beta to create poly-ala > > fab AAAAAAA, pol > > # create copy of the polymer > > create copy, pol > > # adjust a torsion > > set_dihedral pol///4/N, pol///4/CA, pol///4/C, pol///5/N, 60 > > # superimpose back on the original copy > > fit pol, copy > > Cheers, > Warren > > ________________________________ > From: Vivek Ranjan [mailto:vran...@gmail.com] > Sent: Tue 6/2/2009 10:57 AM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] reorienting a chain > > Hello, > > I have a long chain of polymer. Once I change some dihedral angles, it > orients in a different direction. I would like the chain to be > reoriented in the same direction as it initially was. Is it possible > within pymol ? How can I achieve this ? > > -- > Thank you and Regards, > > Vivek Ranjan > > ------------------------------------------------------------------------------ > OpenSolaris 2009.06 is a cutting edge operating system for enterprises > looking to deploy the next generation of Solaris that includes the latest > innovations from Sun and the OpenSource community. Download a copy and > enjoy capabilities such as Networking, Storage and Virtualization. > Go to: http://p.sf.net/sfu/opensolaris-get > _______________________________________________ > 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 > > > > -- Thank you and Regards, Vivek Ranjan ------------------------------------------------------------------------------ OpenSolaris 2009.06 is a cutting edge operating system for enterprises looking to deploy the next generation of Solaris that includes the latest innovations from Sun and the OpenSource community. Download a copy and enjoy capabilities such as Networking, Storage and Virtualization. Go to: http://p.sf.net/sfu/opensolaris-get _______________________________________________ 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
