Hi Yawen, Yes, some atoms are left out. Please see the PyMOLWiki "align" page (http://pymolwiki.org/index.php/Align) or type "help align" for more information. If you want to fit given pairs of atoms, please use fit or its appropriate variation ("help fit" in PyMOL) or the fit page on the PyMOLWiki (http://pymolwiki.org/index.php/Fit).
Cheers, -- Jason 2010/8/16 Thomas Juettemann <juettem...@gmail.com>: > This question fits better the pymol list. > > > ---------- Forwarded message ---------- > From: 李雅雯 <yaya_beih...@yahoo.com.cn> > Date: 16 August 2010 12:31 > Subject: pdb-l: one question about using pymol > To: pd...@sdsc.edu > > > Hi, thanks for your attention. > > I am using pymol to do structural alignment. Pymol will return this sentence > " ExecutiveRMS: 4 atoms rejected during cycle 1 (RMS=0.34). > ExecutiveRMS: 3 atoms rejected during cycle 2 (RMS=0.27)." > while it returns the RMSD value. > > I do not understand what does this mean. why there are two cycles? 4 > atoms rejected? does this mean those 4 atoms are not calculated? > > Thanks for helping me > > Yawen > > > > > > TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see > https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . > > ------------------------------------------------------------------------------ > This SF.net email is sponsored by > > Make an app they can't live without > Enter the BlackBerry Developer Challenge > http://p.sf.net/sfu/RIM-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 -- Jason Vertrees, PhD PyMOL Product Manager Schrodinger, LLC (e) jason.vertr...@schrodinger.com (o) +1 (603) 374-7120 ------------------------------------------------------------------------------ This SF.net email is sponsored by Make an app they can't live without Enter the BlackBerry Developer Challenge http://p.sf.net/sfu/RIM-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
