There are two filter command line in your tutorial:
awk ‘{if (NF==13 && $5>40) print $0; if (NF==14 && $6>40) print $0}’
awk ‘{if (NF==13 && ($7>40 || $9>40)) printf "%s ",$3; if (NF==14 && ($8>40 || $10>40)) printf "%s ",$4}’
It seems that the first command is more strict and filter out less residues.
What are the situations that are suited to this two filter commad.
The first one considers the full residue accessibly, the second one considers both backbone and side-chains accessibilities.
I would go for the second one.
And the 40% cutoff is also not a hard value.
Always good to visualise what you are selecting