ATOM   1489  CA AARG A 181      21.615  11.671  -0.581  0.50 14.29 
ATOM   1490  C  AARG A 181      21.176  11.705   0.880  0.50 13.13 
ATOM   1491  O  AARG A 181      21.097  10.666   1.534  0.50 11.72 
ATOM   1492  CB AARG A 181      20.905  10.524  -1.299  0.50 15.58
ATOM   1493  CG AARG A 181      19.464  10.823  -1.680  0.50 18.22
ATOM   1494  CD AARG A 181      19.399  11.628  -2.968  0.50 21.19 
ATOM   1495  NE AARG A 181      20.181  10.979  -4.017  0.50 24.97
ATOM   1496  CZ AARG A 181      19.785  10.842  -5.278  0.50 25.56 
ATOM   1497  NH1AARG A 181      18.606  11.311  -5.660  0.50 27.74 
ATOM   1498  NH2AARG A 181      20.567  10.230  -6.156  0.50 25.96 
ATOM   1499  N  BARG A 181      23.059  11.454  -0.580  0.50 14.86 
ATOM   1500  CA BARG A 181      21.613  11.672  -0.589  0.50 14.84
ATOM   1501  C  BARG A 181      21.172  11.705   0.874  0.50 13.78 
ATOM   1502  O  BARG A 181      21.092  10.664   1.525  0.50 13.73
ATOM   1503  CB BARG A 181      20.908  10.523  -1.319  0.50 18.29 
ATOM   1504  CG BARG A 181      19.470  10.822  -1.731  0.50 22.11 
ATOM   1505  CD BARG A 181      19.428  11.725  -2.959  0.50 23.55
ATOM   1506  NE BARG A 181      19.985  11.063  -4.138  0.50 24.53  
ATOM   1507  CZ BARG A 181      19.322  10.200  -4.904  0.50 23.44 
ATOM   1508  NH1BARG A 181      18.062   9.888  -4.628  0.50 21.30 
ATOM   1509  NH2BARG A 181      19.926   9.642  -5.944  0.50 24.00

1      2     3  45   6 7        8

##</code><code>##

my $rx_altloc = qr/
   ^(ATOM.{9}   # match only atom records
    (.{3})      # capture atom name (and any space included)
    (.)         # capture alternate location identifier
    \w{3}       # match the amino acid name
    (.{6})      # capture chain and residue number
    .+$ [\r\n]) # match the rest of the line
   (?:(^ATOM.{9} # make sure the next line(s) is an atom record
   (?=\2).{3}    # make sure same atom name
   (?!\3).       # make sure different alternate location
   \w{3}         # don't care if it's the same residue type
   (?=\4).{6}    # make sure it's the same chain and residue
   .+$ [\r\n])+) # match the rest of the line
   (?{
      $altloc = $3;
   })
/xm;
...

$file_contents =~ s/$rx_altloc/$1/g;
/xm;

##</code><code>##

my $rx_altloc_groupByAlt = qr/
   #(?=
   (^ATOM.{9}(.{3})(\w)\w{3}(.{6}).+$ [\r\n])
   ((?:^.+$ [\r\n])*)
   #)
   (ATOM.{9}\2(?!\3).\w{3}\4.+$ [\r\n])
   (?{
      $altloc = $3;
   })
/xm;

...

$file_contents =~ s/$rx_altloc_groupByAlt//g;