Hi Cedric, I suggest to create an alignment object, then you see which atoms got paired.
http://pymolwiki.org/index.php/Align#Alignment_Objects Hope that helps. Cheers, Thomas On 20 Oct 2014, at 11:44, Cedric <patrick.coss...@inbox.com> wrote: > Hi Thomas, > > Thank you, I tried that and it is now 1.9A, still seems high when the overall > RMSD is 0.38 ! > > But, that is definitely something I will keep in mind in the future when > calculating the RMSD. > > Cedric > >> -----Original Message----- >> From: thomas.hol...@schrodinger.com >> Sent: Mon, 20 Oct 2014 11:38:41 -0400 >> To: patrick.coss...@inbox.com >> Subject: Re: [PyMOL] RMSD >> >> 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
