#!/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