Thomas, If PyMOL has paired two atoms for alignment, then they will be used in the calculation of the RMSD.
Also, this sounds like you should be using 'fit' or 'optAlign' to be superposing the molecules. (If you already know the atom pairings, no 'alignment' step is necessary.) Possibly helpful link: http://www.pymolwiki.org/index.php/Category:Structure_Alignment See: fit, optAlign, intra_fit_rms. Hope this helps, -- Jason -- Jason Vertrees, PhD PyMOLWiki -- http://www.pymolwiki.org On Tue, Dec 29, 2009 at 1:27 PM, Thomas Evangelidis <te8...@mbg.duth.gr> wrote: > Dear pymol users, > > I'm trying to understand how align command measures the RMSD between 2 > homologues and explain the discrepancy between that value and the one > obtained from ProFit. The sequence alignments produced by both > programs are continuous and match, but the RMS values are 1.781 and > 4.615 for Pymol and Profit respectively. The RMS corresponds to Ca > atoms only (pymol command line: "align 3G5U_A and name CA and chain A, > H_ABCB1_NBD1 and name CA, cycles=0, object=ao"). Does pymol consider > only Ca atoms that are closer than a default cutoff distance only > (e.g. 5 A) when calculating the RMSD? > > > ------------------------------------------------------------------------------ > This SF.Net email is sponsored by the Verizon Developer Community > Take advantage of Verizon's best-in-class app development support > A streamlined, 14 day to market process makes app distribution fast and easy > Join now and get one step closer to millions of Verizon customers > http://p.sf.net/sfu/verizon-dev2dev > _______________________________________________ > 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 > ------------------------------------------------------------------------------ This SF.Net email is sponsored by the Verizon Developer Community Take advantage of Verizon's best-in-class app development support A streamlined, 14 day to market process makes app distribution fast and easy Join now and get one step closer to millions of Verizon customers http://p.sf.net/sfu/verizon-dev2dev _______________________________________________ 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
