Dear pymol users, I'm trying to understand how align command measures the RMSD between 2 homologues and explain the discrepancy between that value and the one obtained from ProFit. The sequence alignments produced by both programs are continuous and match, but the RMS values are 1.781 and 4.615 for Pymol and Profit respectively. The RMS corresponds to Ca atoms only (pymol command line: "align 3G5U_A and name CA and chain A, H_ABCB1_NBD1 and name CA, cycles=0, object=ao"). Does pymol consider only Ca atoms that are closer than a default cutoff distance only (e.g. 5 A) when calculating the RMSD?
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