Carlos, The complication is that align outputs RMS values for only those atomic pairs remaining following sequence matching following by a refined structure alignment (which omits atoms above a cutoff), whereas rms outputs the value for all atoms matched by identifier (without any optimization).
To run align without optimization, issue: align selection1, selection2, cycles=0 where selection1 and selection2 are replaced with your atom selections, but remember that unmatched residues will not be included in the output RMS value. Cheers, Warren > -----Original Message----- > From: Carlos Ríos Vera [mailto:crosv...@gmail.com] > Sent: Monday, August 24, 2009 1:44 PM > To: pymol-users@lists.sourceforge.net > Subject: [PyMOL] RMS > > Hello people, > > I'm trying to use pymol from a custom python scrypt. What I have done > is to align two structures, but I need get the RMS value from that > align but I have no idea how to do it. > > I tried to use the RMS command but the value differs from the value > that I get from the align. > > Any Idea how to get that value? > > cheers > > ps: Sorry if my English is not so good > > -- > http://crosvera.blogspot.com > > Carlos Ríos V. > Estudiante de Ing. (E) en Computación e Informática. > Universidad del Bío-Bío > VIII Región, Chile > > Linux user number 425502 > > -------------------------------------------------------------------------- > ---- > Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30- > Day > trial. Simplify your report design, integration and deployment - and focus > on > what you do best, core application coding. Discover what's new with > Crystal Reports now. http://p.sf.net/sfu/bobj-july > _______________________________________________ > 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 > > > ------------------------------------------------------------------------------ Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july _______________________________________________ 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
