Hi James, PyMOL can do what you want, but you need to monitor the scientific validity at each step.
First load all your proteins into PyMOL. If that must happen in one command, please see LoadDir (http://pymolwiki.org/index.php/LoadDir). Next, for the target protein with no insertion, let's call it "target", select A > Align > all to this. This should align the objects to "target" and create a new object called "aln_all_to_target". Last, select/remove those atoms in the other proteins and not in the alignment: select toRemove, (not target) and (not aln_all_to_target) remove toRemove You need to ensure that the alignment object truly picked up the correct regions: do not blindly remove atoms without first inspecting them. Cheers, -- Jason On Tue, Nov 1, 2011 at 2:25 PM, James Starlight <jmsstarli...@gmail.com> wrote: > Dear Pymol Users! > > > I want to solve one methodologycal problem via Pymol. I have 20 x-ray > structures of one protein presented in different conformations. > The main problem is that all those structures consist of Hen Lysozyme > inserted in the protein for the improvement of the crystallographic > properties of those structures. > > > I want to load my all 20 tructures in PyMol by one command from worked dir > and make alignment of that enssemble with one structure where there is no > such insertion. As the consequence b this algorithm I want detect lyzocyme > insertion in all my structures wich I want to deleate. > > How I could realize all that via PyMol console ? > > James > > ------------------------------------------------------------------------------ > RSA® Conference 2012 > Save $700 by Nov 18 > Register now! > http://p.sf.net/sfu/rsa-sfdev2dev1 > _______________________________________________ > 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 ------------------------------------------------------------------------------ RSA® Conference 2012 Save $700 by Nov 18 Register now! http://p.sf.net/sfu/rsa-sfdev2dev1 _______________________________________________ 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
