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. ____________________________________________________________ FREE 3D EARTH SCREENSAVER - Watch the Earth right on your desktop! Check it out at http://www.inbox.com/earth ------------------------------------------------------------------------------ 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
