Ignore this question, I found the answer it setting cycles=0.
Thank you
-----Original Message-----
From: patrick.coss...@inbox.com
Sent: Fri, 3 Oct 2014 07:55:31 -0800
To: pymol-users@lists.sourceforge.net
Subject: [PyMOL] align and RMSD calculationHi everyone,I was using align in PYMOL and wanted to calculate RMSD.But, PYMOL gave the following result:MatchAlign: aligning residues (696 vs 696)...ExecutiveAlign: 2177 atoms aligned.ExecutiveRMS: 73 atoms rejected during cycle 1 (RMS=0.38).ExecutiveRMS: 103 atoms rejected during cycle 2 (RMS=0.13).ExecutiveRMS: 105 atoms rejected during cycle 3 (RMS=0.08).ExecutiveRMS: 66 atoms rejected during cycle 4 (RMS=0.07).ExecutiveRMS: 32 atoms rejected during cycle 5 (RMS=0.07).Executive: RMS = 0.063 (1798 to 1798 atoms)How can I calculate the RMS WITHOUT PYMOL throwing atoms away in attempt to improve the RMS?I want the raw number.Thank you
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