Hey Warren, world,
I want to make sure that I understand the output from the align command
correctly. Here is an example:
align (protein1 and name ca), (protein2 and name ca)
Match: read scoring matrix.
Match: assigning 3194 x 3010 pairwise scores.
MatchAlign: aligning residues (3194 vs 3010
Andreas
> ExecutiveAlign: 2889 atoms aligned.
> ExecutiveRMS: 95 atoms rejected during cycle 1 (RMS=6.10).
> ExecutiveRMS: 152 atoms rejected during cycle 2 (RMS=2.98).
means:
2889 atoms were aligned intially, then after looking at the quality of the
alignment, 95 atoms were rejected as outli
