Hello, I tried the following with your advice:
(i) load select.pdb (ii) @beauty.pdb (iii) @script.pdb (iv) save 165.pdb (v) orient select (vi) cmd.matrix_copy(None, "select") (vii) reset (viii) save new.pdb There is no difference in 165.pdb and new.pdb. Let me be clear: Once I change some of the dihedrals in select.pdb, the resulting 165.pdb is oriented in an arbitrary direction. I want to reorient it along one of the axes (preferably along the original Y-axis) and save the resulting coordinates. No matter what I do, I get the same output file. Is there a way. I have attached all the files I am using, in case someone wants to see and comment. Basically, I want to (a) change dihedrals in select.pdb, (b) resulting in 165.pdb, (c) and rotate 165.pdb back to align with select.pdb and save the coordinates of aligned molecule to new.pdb. Please let me know if it can be done. Thank you, Vivek Ranjan On Wed, Jun 3, 2009 at 5:17 PM, Warren DeLano<war...@delsci.com> wrote: > Vivek, > > Please see the example I posted today for Sean Law -- the cmd.matrix_copy > command embedded therein (followed by "reset") performs exactly the action > you're looking for. > > Cheers, > Warren > ________________________________ > From: Vivek Ranjan [mailto:vran...@gmail.com] > Sent: Wed 6/3/2009 9:26 AM > To: Warren DeLano > Cc: pymol-users@lists.sourceforge.net > Subject: Re: [PyMOL] reorienting a chain > > 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 > > > > -- Thank you and Regards, Vivek Ranjan
select.pdb
Description: Protein Databank data
165.pdb
Description: Protein Databank data
beauty.pml
Description: Binary data
script.pml
Description: Binary data
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