Evan,
You can save the "alignment" object resulting from an align command to an
aln file:
align sele1, sele2, object=aln_obj
save alignment.aln, aln_obj
Cheers,
Warren
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> -Original Message-
> From: pymol-u
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
