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