in reply to read between two strings

You could use the flip-flop operator to skip lines which are not between the %%Atom Coords and %%End Frame markers. Maybe something like this?

#!/usr/bin/perl -w use strict; while (<DATA>) { #-- Skip lines not in the section to be processed next unless /^%%Atom Coords/../^%%End Frame/; #-- Skip the section markers next if (/^%%Atom Coords/ or /^%%End Frame/); #-- Parse lines... print; } __DATA__ %%Atom Coords -1.13 12.16 6.15 %%End Frame more stuff... and more stuff... %%Atom Coords -2.26 24.32 12.30 %%End Frame