Hi Cedric, you probably include random waters with "name o". Try adding "... and polymer" to your selection string.
Cheers, Thomas On 20 Oct 2014, at 11:16, Cedric <patrick.coss...@inbox.com> wrote: > Hi, > > I was comparing two very similar structures and I got the following results: > > align pdb1, pdb2, cycles=0 > > 0.38 > > align pdb1, pdb2 and name ca, cycles=0 > 0.05 > > align pdb1, pdb2 and name ca+cb+c+n, cycles=0 > 0.07 > > > align pdb1, pdb2 and name ca+cb+c+n+o, cycles=0 > 9.8 > > I wonder why the addition of the O atom increases the RMSD so much esp when > all atom RMSD is only 0.38A. > > Thank you -- Thomas Holder PyMOL Developer Schrödinger, Inc. ------------------------------------------------------------------------------ Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho _______________________________________________ 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
