In the Madhusudhan paper, the cutoff was at least 70% for a SO of 3.5 A.
Do you mean the SO was 70% for a cutoff of 3.5A?
What number does that correspond to in the salign output?
The percentage of equivalent (i.e. within the cutoff) positions is the
qscorepct member of the SalignData object returned by salign(). Set the
cutoff with the rms_cutoff argument. And make sure you have QUALITY in
the output argument.
For the quality score, is there an objective number that I can use for
every alignment to see whether it is good or not?
As I said, only for structure alignments.
Lastly, for "iterative salign," is it recommended to run the regular
version first or just jump straight to using the iterative salign? The
Madhusudhan paper seems to forgo the use of iterative salign if the
alignment is 70% at a SO of 3.5
I'm assuming you're looking at fig 1 in the paper here. There are three
iterative procedures within that flowchart; one of them is skipped if
the first procedure (simpler alignment using a subset of features) found
a reasonable starting guess for the last procedure (structural
alignment). The second procedure is simply an attempt to improve this
guess if the first failed.