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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