diff --git a/pdbtools/pdb_selaltloc.py b/pdbtools/pdb_selaltloc.py
index 7067672..f4b5181 100644
--- a/pdbtools/pdb_selaltloc.py
+++ b/pdbtools/pdb_selaltloc.py
@@ -26,12 +26,18 @@
 are processed by the script. If you select -A and an atom has conformers with
 altlocs B and C, both B and C will be kept in the output.
 
+Despite not an official format, many times alternative locations are identified
+by a blank character ' ' (space), and a character, for example ('A'). In these
+cases, to select the alternative location identified by a blank character,
+define blank in the command line, see below.
+
 Usage:
     python pdb_selaltloc.py [-<option>] <pdb file>
 
 Example:
     python pdb_selaltloc.py 1CTF.pdb  # picks locations with highest occupancy
     python pdb_selaltloc.py -A 1CTF.pdb  # picks alternate locations labelled 'A'
+    python pdb_selaltloc.py -' ' 1CTF.pdb  # picks alternate locations labelled blank ' '
 
 This program is part of the `pdb-tools` suite of utilities and should not be
 distributed isolatedly. The `pdb-tools` were created to quickly manipulate PDB
@@ -114,338 +120,206 @@ def check_input(args):
     return (fh, option)
 
 
-def select_by_occupancy(fhandle):
-    return select_altloc(fhandle, selloc=None, byocc=True)
-
-
-def select_by_altloc(fhandle, selloc):
-    return select_altloc(fhandle, selloc, byocc=False)
-
-
-def select_altloc(fhandle, selloc=None, byocc=False):
+def run(fhandle, option=None):
     """
-    Pick one altloc when atoms have more than one.
-
-    If the specified altloc (selloc) is not present for this particular
-    atom, outputs all altlocs. For instance, if atom X has altlocs A and
-    B but the user picked C, we return A and B anyway. If atom Y has
-    altlocs A, B, and C, then we only return C.
-
-    This function is a generator.
+    Selects altloc labels for the entire PDB file.
 
     Parameters
     ----------
     fhandle : an iterable giving the PDB file line-by-line.
 
-    Yields
-    ------
-    str (line-by-line)
-        The PDB file with altlocs according to selection.
-    """
-    if selloc is None and not byocc:
-        raise ValueError('Provide either `selloc` or `byocc`.')
-
-    altloc_lines = dict()  # dict to capture the lines from a altloc group
-    res_per_loc = dict()  # dict to capture the residues per altloc group
+    option : str or `None`.
+        The alternative location identifier to select. By default
+        (`None`) selects the alternative location with highest
+        occupancy. In this case, if the different alternative locations
+        have the same occupancy, selects the one that comes first.
+        Selecting by highest occupancy removes all altloc labels for all
+        atoms. Provide an option (e.g. 'A') to select only atoms with
+        altloc label `A`. If you select `A` and an atom has conformers
+        with altlocs `B` and `C`, both B and C will be kept in the
+        output. Despite not an official format, many times alternative
+        locations are identified by a blank character ' ' (space), and a
+        [A-Z] character.  In these cases, to select the alternative
+        location identified by a blank character give `option=' '`.
 
-    prev_altloc = ''
-    prev_resname = ''
-    prev_resnum = ''
+    Returns
+    -------
+    generator
+        A generator object. To exhaust the generator, that is, to
+        process the PDB file (or PDB lines), convert it to a list.
 
-    # uses the same function names in the loop below. However, depending
-    # on the input options, the functions used are different. One is
-    # specific for byocc=True, and other specific for occ char selection
-    flush_func_multi_residues = flush_resloc_occ if byocc else flush_resloc
+        >>> from pdbtools.pdb_selaltloc import run
+        >>> with('input.pdb', 'r') as fin:
+        >>>     processed_lines = list(run(fin))
 
-    flush_func_single_residues = \
-        flush_resloc_occ_same_residue if byocc else flush_resloc_id_same_residue
+        For more example see:
 
-    # defines records and terminators
+        >>> import pdbtools
+        >>> help(pdbtools)
+    """
     records = ('ATOM', 'HETATM', 'ANISOU')
-    terminators = ('TER', 'END', 'CONECT', 'END', 'ENDMDL')
+    terminators = ('TER', 'END', 'CONECT', 'END', 'ENDMDL', 'MODEL')
+
+    # register atom information
+    register = dict()
+
+    # register comment lines
+    others = []
+
+    # register current chain
+    chain = None
+    prev_chain = None
 
+    # keep record of the line number. This will be used to sort lines
+    # after selecting the desired alternative location
+    nline = 0
+
+    # the loop will collect information on the different atoms
+    # throughout the PDB file until a new chain or any terminal line is
+    # found. At that point, the collected information is flushed because
+    # all altlocs for that block have been defined.
     for line in fhandle:
+        nline += 1
 
         if line.startswith(records):
-            # captures the relevant parameters
-            altloc = line[16]
-            resname = line[17:20]
-            resnum = line[22:26].strip()
-
-            if is_another_altloc_group(
-                    altloc, prev_altloc, resnum, prev_resnum,
-                    resname, prev_resname, altloc_lines, res_per_loc):
-                # if we see the altloc group has changed, we should flush
-                # the lines observed for the previous altloc group
-
-                # uses "for loop" instead of "yield from" to maintain
-                # compatibility with older python version
-                if partial_altloc(altloc_lines):
-                    flush_func = flush_func_single_residues
-                else:
-                    flush_func = flush_func_multi_residues
 
-                for __line in flush_func(selloc=selloc, altloc_lines=altloc_lines):
-                    yield __line
+            # here resnum + insertion code are taken to identify
+            # different residues
+            resnum = line[22:27]
+            atomname = line[12:16]
+            altloc = line[16]
+            chain = line[21:22]
 
-                altloc_lines = dict()
-                res_per_loc = dict()
+            # flush lines because we enter a new chain
+            if chain != prev_chain:
+                # the "yield from" statement is avoided to keep
+                # compatibility with Python 2.7
+                for _line in _flush(register, option, others):
+                    yield _line
 
-            # saves the line per altloc identifier
-            current_loc = altloc_lines.setdefault(altloc, [])
-            current_loc.append(line)
+                # Python 2.7 compatibility. Do not use .clear() method
+                # restart help variables
+                del register, others
+                register, others = dict(), []
 
-            # registers which residues are seen for each identifier
-            rploc = res_per_loc.setdefault(altloc, set())
-            rploc.add((resname, resnum))
+            # organizes information hierarchically
+            resnum_d = register.setdefault(resnum, {})
+            atomname_d = resnum_d.setdefault(atomname, {})
+            altloc_d = atomname_d.setdefault(altloc, [])
 
-            prev_altloc = altloc
-            prev_resnum = resnum
-            prev_resname = resname
+            # adds info to dictionary
+            altloc_d.append((nline, line))
 
+        # flush information because we reached the end of a block
         elif line.startswith(terminators):
-            # before flushing the terminator line
-            # we should flush the previous altloc group
-            if altloc_lines:
-                if partial_altloc(altloc_lines):
-                    flush_func = flush_func_single_residues
-                else:
-                    flush_func = flush_func_multi_residues
-                for __line in flush_func(selloc=selloc, altloc_lines=altloc_lines):
-                    yield __line
-
-                altloc_lines = dict()
-                res_per_loc = dict()
+            for _line in _flush(register, option, others):
+                yield _line
 
-            prev_altloc = ''
-            prev_resname = ''
-            prev_resnum = ''
+            del register, others
+            register, others = dict(), []
 
-            yield line  # the terminator line
+            yield line  # yield the current line after flush
 
         else:
-            prev_altloc = ''
-            prev_resname = ''
-            prev_resnum = ''
-            yield line
+            # append comments to flush list
+            # The reason to add comments to a list instead of yielding
+            # them directly is to cover the possibility of having
+            # comments in the middle of the PDB file. Obviously is this
+            # extremely unlikely. But just in case...
+            others.append((nline, line))
 
-    # end of for loop
-    # flush altloc residues in case the last residue was an altloc
-    if altloc_lines:
+        prev_chain = chain
 
-        if partial_altloc(altloc_lines):
-            flush_func = flush_func_single_residues
-        else:
-            flush_func = flush_func_multi_residues
-
-        for __line in flush_func(selloc=selloc, altloc_lines=altloc_lines):
-            yield __line
-
-        altloc_lines = []
-        res_per_loc = dict()
-
-
-def is_another_altloc_group(
-        altloc,
-        prev_altloc,
-        resnum,
-        prev_resnum,
-        resname,
-        prev_resname,
-        altloc_lines,
-        rploc
-):
-    """Detect if current line belongs to a new altloc group."""
-    a0 = prev_altloc
-    a1 = altloc
-    ra0 = prev_resname
-    ra1 = resname
-    ru0 = prev_resnum
-    ru1 = resnum
-    rl = altloc_lines
-    rv = list(rploc.values())
-
-    is_another = (
-        all((a0, ra0, ru0)) and (
-            (a0 != a1 and a1 == ' ' and ru1 > ru0)
-            or (a0 == ' ' and a1 != ' ' and ru1 > ru0)
-            or (a0 == ' ' and a1 == ' ' and (ru1 != ru0 or ra1 != ra0))
-            or (
-                a0 == a1
-                and a0 != ' '
-                and a1 in rl
-                and ru1 > ru0
-                and len(rl) > 1
-                and all(len(v) == len(rv[0]) for v in rv[1:])
-            )
-        )
-    )
-
-    return is_another
-
-
-def flush_resloc(selloc, altloc_lines):
-    """Flush the captured altloc lines."""
-    # only the selected altloc is yieled
-    if selloc in altloc_lines:
-        for line2flush in altloc_lines[selloc]:
-            yield line2flush[:16] + ' ' + line2flush[17:]
-
-    # the altloc group does not contain the selected altloc
-    # therefore, all members should be yielded
-    else:
-        for key, lines2flush in altloc_lines.items():
-            for line2flush in lines2flush:
-                yield line2flush
-
-
-def flush_resloc_occ(altloc_lines, **kw):
-    """Flush the captured altloc lines by highest occupancy."""
-    # only the selected altloc is yieled
-    highest = 0.00
-    altloc = ' '
-
-    # detects which altloc identifier has the highest occupancy
-    for key, lines2flush in altloc_lines.items():
-        # we check only the first line because all atoms in one identifier
-        # should have the same occupancy value
-        occ = float(lines2flush[0][54:60])
-        if occ > highest:
-            altloc = key
-            highest = occ
-
-    for line2flush in altloc_lines[altloc]:
-        yield line2flush[:16] + ' ' + line2flush[17:]
-
-
-def flush_resloc_id_same_residue(selloc, altloc_lines):
-    """Flush altloc if altloc are atoms in the same residue - by ID."""
-    # places all lines in a single list
-    sorted_atoms = _get_sort_atoms(altloc_lines)
-
-    for atom, linet in sorted_atoms:
-        to_yield = []
-        # remember linet is a tuple, where the first item is the atom number
-        lines = linet[1]
-
-        # here we don't need to care about anisou lines as in
-        # `flush_resloc_occ_same_residue` because ATOM/HETATM and ANISOU
-        # are already sorted by definition and lines are yieled from the
-        # altloc record
-        for line in lines:
-            if line[16] == selloc:
-                to_yield.append(line)
-
-        if to_yield:
-            for line in to_yield:
-                yield line[:16] + ' ' + line[17:]
-        else:
-            for line in lines:
-                yield line
+    # at the end of the PDB, flush the remaining lines
+    for _line in _flush(register, option, others):
+        yield _line
 
 
-def flush_resloc_occ_same_residue(altloc_lines, **kw):
-    """Flush altloc if altloc are atoms in the same residue - by occ."""
-    sorted_atoms = _get_sort_atoms(altloc_lines)
+def _flush(register, option, others):
+    """
+    Processes the collected atoms according to the selaltloc option.
+    """
+    lines_to_yield = []
+    select_by_occupancy = option is None
 
-    for atom, linest in sorted_atoms:
-        lines = linest[1]
+    atom_lines = ('ATOM', 'HETATM')
 
-        atom_lines = [ln for ln in lines if ln.startswith(("ATOM", "HETATM"))]
-        anisou_lines = [ln for ln in lines if ln.startswith(("ANISOU"))]
+    # anisou lines are treated specially
+    anisou_lines = ('ANISOU',)
 
-        if anisou_lines:
-            new = []
+    for resnum, atomnames in register.items():
 
-            if len(atom_lines) != len(anisou_lines):
-                emsg = (
-                    "There is an error with this PDB. "
-                    "We expect one ANISOU line per ATOM/HETATM lines. "
-                    "But the number of ATOM/HETATM and ANISOU lines differ."
-                )
-                raise ValueError(emsg)
+        for atomname, altlocs in atomnames.items():
 
-            for _a, _b in zip(atom_lines, anisou_lines):
-                new.append((_a, _b))
+            if select_by_occupancy:
 
-            new.sort(key=lambda x: float(x[0][54:60]), reverse=True)
+                # gathers all alternative locations for the atom
+                all_lines = []
+                for altloc, lines in altlocs.items():
+                    all_lines.extend(lines)
 
-            # ATOM/HETATM
-            yield new[0][0][:16] + ' ' + new[0][0][17:]
-            # ANISOU
-            yield new[0][1][:16] + ' ' + new[0][1][17:]
+                # identifies the highest occupancy combining dictionary
+                # and sorting
+                new = {}
+                for line_number, line in all_lines:
+                    if line.startswith(atom_lines):
+                        occupancy_number = line[54:60]
+                        list_ = new.setdefault(occupancy_number, [])
+                        list_.append((line_number, line))
 
-        else:
-            atom_lines.sort(key=lambda x: float(x[54:60]), reverse=True)
-            yield atom_lines[0][:16] + ' ' + atom_lines[0][17:]
-
-
-def _get_sort_atoms(altloc_lines):
-    # this function is used by both:
-    # flush_resloc_occ_same_residue
-    # flush_resloc_id_same_residue
-    all_lines = []
-    for altloc, lines in altloc_lines.items():
-        all_lines.extend(lines)
-
-    # organize by atoms
-    atoms = dict()
-    # key in the dictionary are unique identifiers of the same residue
-    for line in all_lines:
-        res_number = int(line[22:26])
-        res_name = line[17:20].strip()
-        atom_name = line[12:16]
-        atom_number = int(line[6:11])
-        chain_id = line[21]
-        key = (res_number, res_name, atom_name, chain_id)
-        # the atom number is saved so that the original order can be kept
-        alist = atoms.setdefault(key, (atom_number, []))
-        alist[1].append(line)
-
-    # entries at this point are not sorted. Sorts entries by residue
-    # number followed by atom number
-    sorted_atoms = sorted(list(atoms.items()), key=lambda x: (x[0][0], x[1][0]))
-    return sorted_atoms
-
-
-def all_same_residue(altloc_lines):
-    """Assert all lines are from same residue."""
-    residues = set()
-    for key, val in altloc_lines.items():
-        for line in val:
-            resname = line[17:20]
-            resnum = line[22:26].strip()
-            residues.add((resname, resnum))
-
-    return len(residues) == 1
-
-
-def partial_altloc(altloc_lines):
-    """Detect if the altloc positions are atoms in a single residue."""
-    return ' ' in altloc_lines and all_same_residue(altloc_lines)
+                    # assumes ANISOU succeed the respective ATOM line
+                    elif line.startswith(anisou_lines):
+                        list_.append((line_number, line))
 
+                # sort keys by occupancy
+                keys_ = sorted(new.keys(), key=lambda x: float(x.strip()), reverse=True)
 
-def run(fhandle, option=None):
-    """
-    Selects altloc labels for the entire PDB file.
+                these_atom_lines = new[keys_[0]]
+                if len(keys_) == 1 and len(these_atom_lines) > 1:
+                    # address "take first if occ is the same"
+                    # see: https://github.com/haddocking/pdb-tools/issues/153#issuecomment-1488627668
+                    lines_to_yield.extend(_remove_altloc(these_atom_lines[0:1]))
 
-    Parameters
-    ----------
-    fhandle : an iterable giving PDB file line-by-line.
+                    # if there's ANISOU, add it
+                    if these_atom_lines[1][1].startswith(anisou_lines):
+                        lines_to_yield.extend(_remove_altloc(these_atom_lines[1:2]))
+
+                # this should run when there are more than one key or
+                # the key has only one atom line. Keys are the occ
+                # value.
+                else:
+                    # when occs are different, select the highest one
+                    lines_to_yield.extend(_remove_altloc(these_atom_lines))
+
+                del all_lines, new
+
+            # selected by option:
+            else:
+                if option in altlocs:
+                    # selects the option, that's it
+                    lines_to_yield.extend(_remove_altloc(altlocs[option]))
+
+                else:
+                    # if the option does not exist, add all altlocs
+                    for altloc, lines in altlocs.items():
+                        lines_to_yield.extend(lines)
+
+    # add comments
+    lines_to_yield.extend(others)
+
+    # lines are sorted to the line number so that the output is sorted
+    # the same way as in the input PDB
+    lines_to_yield.sort(key=lambda x: x[0])
+
+    # the line number is ignored, only the line is yield
+    for line_number, line in lines_to_yield:
+        yield line
 
-    Returns
-    -------
-    generator
-        If option is None, return `select_by_occupancy` generator.
-        If option is given, return `select_by_altloc` generator.
-        See `pdb_selaltloc.select_by_occupancy` and
-        `pdb_selaltloc.select_by_altloc` for more details.
-    """
-    if option is None:
-        return select_by_occupancy(fhandle)
 
-    else:
-        return select_by_altloc(fhandle, option)
+def _remove_altloc(lines):
+    # the altloc ID is removed in processed altloc lines
+    for line_num, line in lines:
+        yield (line_num, line[:16] + ' ' + line[17:])
 
 
 def main():
diff --git a/tests/data/altloc_3B9F.pdb b/tests/data/altloc_3B9F.pdb
new file mode 100644
index 0000000..98d8b2d
--- /dev/null
+++ b/tests/data/altloc_3B9F.pdb
@@ -0,0 +1,133 @@
+PDBTLS   This file was edited to test pdb_selaltloc
+PDBTLS   Original PDB 3B9F
+PDBTLS
+HEADER    HYDROLASE/HYDROLASE INHIBITOR           05-NOV-07   3B9F              
+TITLE     1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX                   
+COMPND  21 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+KEYWDS   4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX             
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    W.LI,T.E.ADAMS,J.A.HUNTINGTON                                         
+REVDAT   1   22-APR-08 3B9F    0                                                
+JRNL        AUTH   W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON           
+REMARK   2                                                                      
+REMARK 999 NATURAL VARIANT AT THIS POSITION                                     
+DBREF  3B9F I   17   387  UNP    P05154   IPSP_HUMAN      36    406             
+SEQADV 3B9F ALA H  195  UNP  P00734    SER   568 ENGINEERED MUTATION            
+SEQRES  31 I  395  LYS VAL ASN ARG PRO                                          
+MODRES 3B9F ASN H   60G ASN  GLYCOSYLATION SITE                                 
+HET    NAG  A   1      14                                                       
+HETNAM     NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE                         
+HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL                                    
+FORMUL  14  HOH   *523(H2 O)                                                    
+HELIX    1   1 ASN L    1K GLY L    1F 1                                   6    
+HELIX   20  20 SER I  305  THR I  309  5                                   5    
+SHEET    1   A 7 SER H  20  ASP H  21  0                                        
+SHEET    2   G 2 GLY I 340  ARG I 342  1  O  THR I 341   N  TRP I 190           
+SSBOND   1 CYS L    1    CYS H  122                          1555   1555  2.03  
+LINK         O6  NAG A   1                 C1  FUC A   2     1555   1555  1.40  
+CISPEP   2 LYS H  185    PRO H  186          0         0.28                     
+CRYST1   44.055   48.825   97.850  78.72  81.52  77.69 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.022699 -0.004951 -0.002582        0.00000                         
+SCALE2      0.000000  0.020963 -0.003616        0.00000                         
+SCALE3      0.000000  0.000000  0.010485        0.00000                         
+ATOM     16  N   TYR L   1P    -35.899  36.071 -57.146  1.00 24.40           N  
+ATOM     17  CA  TYR L   1P    -35.533  35.711 -55.782  1.00 22.98           C  
+ATOM     18  C   TYR L   1P    -35.689  36.923 -54.879  1.00 22.73           C  
+ATOM     19  O   TYR L   1P    -35.212  38.013 -55.199  1.00 24.86           O  
+ATOM     28  N  AGLN L   1O    -36.361  36.722 -53.750  0.20 22.43           N  
+ATOM     29  N  BGLN L   1O    -36.368  36.734 -53.754  0.80 21.82           N  
+ATOM     30  CA AGLN L   1O    -36.584  37.781 -52.773  0.23 21.92           C  
+ATOM     31  CA BGLN L   1O    -36.567  37.813 -52.796  0.77 21.45           C  
+ATOM     32  C  AGLN L   1O    -35.689  37.523 -51.567  0.25 21.18           C  
+ATOM     33  C  BGLN L   1O    -35.688  37.528 -51.586  0.65 20.57           C  
+ATOM     34  O  AGLN L   1O    -35.816  36.492 -50.908  0.23 20.76           O  
+ATOM     35  O  BGLN L   1O    -35.820  36.482 -50.950  0.77 19.47           O  
+ATOM     46  N   THR L   1N    -34.783  38.453 -51.279  1.00 20.45           N  
+ATOM     47  CA  THR L   1N    -33.885  38.283 -50.143  1.00 20.33           C  
+ATOM     48  C   THR L   1N    -34.665  38.284 -48.834  1.00 20.94           C  
+ATOM     49  O   THR L   1N    -35.715  38.926 -48.718  1.00 20.47           O  
+ATOM    101  N   THR L   1H    -25.711  41.829 -41.231  1.00 16.46           N  
+ATOM    102  CA  THR L   1H    -25.418  40.733 -40.321  1.00 14.66           C  
+ATOM    103  C   THR L   1H    -25.179  39.417 -41.051  1.00 15.08           C  
+ATOM    104  O   THR L   1H    -24.467  38.557 -40.552  1.00 14.35           O  
+ATOM    123  N  ASER L   1E    -22.556  39.135 -47.649  0.10 14.32           N  
+ATOM    124  N  BSER L   1E    -22.558  39.094 -47.639  0.85 13.30           N  
+ATOM    125  CA ASER L   1E    -23.019  39.209 -49.032  0.16 13.53           C  
+ATOM    126  CA BSER L   1E    -23.010  39.174 -49.023  0.84 12.40           C  
+ATOM    127  C  ASER L   1E    -23.259  37.839 -49.653  0.10 13.43           C  
+ATOM    128  C  BSER L   1E    -23.296  37.813 -49.635  0.82 12.51           C  
+ATOM    129  O  ASER L   1E    -22.829  36.818 -49.115  0.34 12.37           O  
+ATOM    130  O  BSER L   1E    -22.933  36.779 -49.072  0.42 11.68           O  
+ATOM    161  N   CYS L   1     -27.779  33.791 -54.663  1.00 11.36           N  
+ATOM    162  CA  CYS L   1     -27.645  32.429 -54.138  1.00 11.72           C  
+ATOM    163  C   CYS L   1     -28.184  31.351 -55.065  1.00 12.46           C  
+ATOM    164  O   CYS L   1     -29.066  31.597 -55.887  1.00 11.13           O  
+ATOM    167  N   GLY L   2     -27.618  30.155 -54.931  1.00 11.94           N  
+ATOM    168  CA  GLY L   2     -28.093  29.010 -55.681  1.00 13.42           C  
+ATOM    169  C   GLY L   2     -27.920  28.936 -57.179  1.00 13.71           C  
+ATOM    170  O   GLY L   2     -28.452  28.010 -57.799  1.00 12.21           O  
+ATOM    171  N   LEU L   3     -27.207  29.893 -57.766  1.00 11.48           N  
+ATOM    172  CA  LEU L   3     -26.960  29.891 -59.207  1.00 12.60           C  
+ATOM    173  C   LEU L   3     -25.462  29.636 -59.346  1.00 13.82           C  
+ATOM    174  O   LEU L   3     -24.649  30.462 -58.944  1.00 14.29           O  
+TER     378      LEU L   3                                                      
+ATOM    498  N  AMET H  32     -15.884  21.898 -46.134  0.03 13.63           N  
+ATOM    499  N  BMET H  32     -15.886  21.863 -46.147  0.84 13.45           N  
+ATOM    500  CA AMET H  32     -15.223  20.827 -45.399  0.10 13.62           C  
+ATOM    501  CA BMET H  32     -15.262  20.752 -45.438  0.90 14.92           C  
+ATOM    502  C  AMET H  32     -14.910  21.331 -44.004  0.01 14.47           C  
+ATOM    503  C  BMET H  32     -14.862  21.255 -44.046  0.99 15.40           C  
+ATOM    504  O  AMET H  32     -14.280  22.376 -43.844  0.10 14.26           O  
+ATOM    505  O  BMET H  32     -14.125  22.236 -43.935  0.67 14.61           O  
+ATOM    514  N   LEU H  33     -15.346  20.594 -42.992  1.00 15.12           N  
+ATOM    515  CA  LEU H  33     -15.057  20.994 -41.613  1.00 17.37           C  
+ATOM    516  C   LEU H  33     -13.966  20.110 -41.025  1.00 21.15           C  
+ATOM    517  O   LEU H  33     -14.053  18.878 -41.092  1.00 21.77           O  
+ATOM    544  N   LYS H  36      -8.375  20.177 -35.426  1.00 47.23           N  
+ATOM    545  CA  LYS H  36      -6.948  20.457 -35.546  1.00 49.79           C  
+ATOM    546  C   LYS H  36      -6.046  19.727 -34.564  1.00 51.19           C  
+ATOM    547  O   LYS H  36      -6.501  19.201 -33.546  1.00 51.77           O  
+ATOM    553  N   SER H  36A     -4.757  19.702 -34.898  0.40 52.14           N  
+ATOM    554  CA  SER H  36A     -3.731  19.057 -34.087  0.40 52.58           C  
+ATOM    555  C   SER H  36A     -4.254  17.826 -33.356  0.40 52.69           C  
+ATOM    556  O   SER H  36A     -4.508  17.868 -32.151  0.40 54.21           O  
+ATOM    553  N  BSER H  36A     -4.757  19.702 -34.898  0.60 52.14           N  
+ATOM    554  CA BSER H  36A     -3.731  19.057 -34.087  0.60 52.58           C  
+ATOM    555  C  BSER H  36A     -4.254  17.826 -33.356  0.60 52.69           C  
+ATOM    556  O  BSER H  36A     -4.508  17.868 -32.151  0.60 54.21           O  
+ATOM    583  N  ALEU H  40     -10.561  15.413 -41.434  0.48 28.25           N  
+ATOM    584  N  BLEU H  40     -10.564  15.370 -41.413  0.48 28.64           N  
+ATOM    585  CA ALEU H  40     -11.939  15.701 -41.811  0.03 25.33           C  
+ATOM    586  CA BLEU H  40     -11.952  15.605 -41.789  0.97 26.04           C  
+ATOM    587  C  ALEU H  40     -12.927  15.248 -40.743  0.13 23.56           C  
+ATOM    588  C  BLEU H  40     -12.860  15.301 -40.605  0.61 24.27           C  
+ATOM    589  O  ALEU H  40     -12.964  14.075 -40.371  0.11 23.23           O  
+ATOM    590  O  BLEU H  40     -12.739  14.255 -39.969  0.89 22.89           O  
+ATOM    599  N  ALEU H  41     -13.727  16.191 -40.255  0.44 21.23           N  
+ATOM    600  N  BLEU H  41     -13.774  16.219 -40.316  0.53 22.16           N  
+ATOM    601  CA ALEU H  41     -14.727  15.903 -39.235  0.04 18.81           C  
+ATOM    602  CA BLEU H  41     -14.696  16.049 -39.204  0.96 19.96           C  
+ATOM    603  C  ALEU H  41     -16.114  15.742 -39.829  0.60 17.12           C  
+ATOM    604  C  BLEU H  41     -16.124  15.865 -39.697  0.40 18.03           C  
+ATOM    605  O  ALEU H  41     -16.804  14.756 -39.572  0.25 16.40           O  
+ATOM    606  O  BLEU H  41     -16.844  14.976 -39.247  0.61 16.77           O  
+ATOM    615  N   CYS H  42     -16.515  16.722 -40.632  1.00 15.17           N  
+ATOM    616  CA  CYS H  42     -17.854  16.716 -41.198  1.00 14.43           C  
+ATOM    617  C   CYS H  42     -17.965  17.557 -42.446  1.00 13.79           C  
+ATOM    618  O   CYS H  42     -17.003  18.181 -42.892  1.00 13.66           O  
+ATOM    621  N   GLY H  43     -19.183  17.574 -42.976  1.00 12.50           N  
+ATOM    622  CA  GLY H  43     -19.506  18.388 -44.128  1.00 13.66           C  
+ATOM    623  C   GLY H  43     -20.155  19.637 -43.546  1.00 12.41           C  
+ATOM    624  O   GLY H  43     -20.400  19.711 -42.333  1.00 11.38           O  
+ATOM    625  N   ALA H  44     -20.433  20.608 -44.408  1.00 12.66           N  
+ATOM    626  CA  ALA H  44     -21.043  21.876 -44.015  1.00 12.16           C  
+ATOM    627  C   ALA H  44     -21.446  22.558 -45.312  1.00 11.20           C  
+ATOM    628  O   ALA H  44     -21.152  22.052 -46.394  1.00 11.04           O  
+TER     630      TER H  44
+CONECT 5572 5571
+MASTER      413    0   12   20   38    0    0    6 5736    3  109   55
+END
diff --git a/tests/data/altloc_3B9F_A.pdb b/tests/data/altloc_3B9F_A.pdb
new file mode 100644
index 0000000..51541b2
--- /dev/null
+++ b/tests/data/altloc_3B9F_A.pdb
@@ -0,0 +1,113 @@
+PDBTLS   This file was edited to test pdb_selaltloc
+PDBTLS   Original PDB 3B9F
+PDBTLS
+HEADER    HYDROLASE/HYDROLASE INHIBITOR           05-NOV-07   3B9F              
+TITLE     1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX                   
+COMPND  21 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+KEYWDS   4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX             
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    W.LI,T.E.ADAMS,J.A.HUNTINGTON                                         
+REVDAT   1   22-APR-08 3B9F    0                                                
+JRNL        AUTH   W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON           
+REMARK   2                                                                      
+REMARK 999 NATURAL VARIANT AT THIS POSITION                                     
+DBREF  3B9F I   17   387  UNP    P05154   IPSP_HUMAN      36    406             
+SEQADV 3B9F ALA H  195  UNP  P00734    SER   568 ENGINEERED MUTATION            
+SEQRES  31 I  395  LYS VAL ASN ARG PRO                                          
+MODRES 3B9F ASN H   60G ASN  GLYCOSYLATION SITE                                 
+HET    NAG  A   1      14                                                       
+HETNAM     NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE                         
+HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL                                    
+FORMUL  14  HOH   *523(H2 O)                                                    
+HELIX    1   1 ASN L    1K GLY L    1F 1                                   6    
+HELIX   20  20 SER I  305  THR I  309  5                                   5    
+SHEET    1   A 7 SER H  20  ASP H  21  0                                        
+SHEET    2   G 2 GLY I 340  ARG I 342  1  O  THR I 341   N  TRP I 190           
+SSBOND   1 CYS L    1    CYS H  122                          1555   1555  2.03  
+LINK         O6  NAG A   1                 C1  FUC A   2     1555   1555  1.40  
+CISPEP   2 LYS H  185    PRO H  186          0         0.28                     
+CRYST1   44.055   48.825   97.850  78.72  81.52  77.69 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.022699 -0.004951 -0.002582        0.00000                         
+SCALE2      0.000000  0.020963 -0.003616        0.00000                         
+SCALE3      0.000000  0.000000  0.010485        0.00000                         
+ATOM     16  N   TYR L   1P    -35.899  36.071 -57.146  1.00 24.40           N  
+ATOM     17  CA  TYR L   1P    -35.533  35.711 -55.782  1.00 22.98           C  
+ATOM     18  C   TYR L   1P    -35.689  36.923 -54.879  1.00 22.73           C  
+ATOM     19  O   TYR L   1P    -35.212  38.013 -55.199  1.00 24.86           O  
+ATOM     28  N   GLN L   1O    -36.361  36.722 -53.750  0.20 22.43           N  
+ATOM     30  CA  GLN L   1O    -36.584  37.781 -52.773  0.23 21.92           C  
+ATOM     32  C   GLN L   1O    -35.689  37.523 -51.567  0.25 21.18           C  
+ATOM     34  O   GLN L   1O    -35.816  36.492 -50.908  0.23 20.76           O  
+ATOM     46  N   THR L   1N    -34.783  38.453 -51.279  1.00 20.45           N  
+ATOM     47  CA  THR L   1N    -33.885  38.283 -50.143  1.00 20.33           C  
+ATOM     48  C   THR L   1N    -34.665  38.284 -48.834  1.00 20.94           C  
+ATOM     49  O   THR L   1N    -35.715  38.926 -48.718  1.00 20.47           O  
+ATOM    101  N   THR L   1H    -25.711  41.829 -41.231  1.00 16.46           N  
+ATOM    102  CA  THR L   1H    -25.418  40.733 -40.321  1.00 14.66           C  
+ATOM    103  C   THR L   1H    -25.179  39.417 -41.051  1.00 15.08           C  
+ATOM    104  O   THR L   1H    -24.467  38.557 -40.552  1.00 14.35           O  
+ATOM    123  N   SER L   1E    -22.556  39.135 -47.649  0.10 14.32           N  
+ATOM    125  CA  SER L   1E    -23.019  39.209 -49.032  0.16 13.53           C  
+ATOM    127  C   SER L   1E    -23.259  37.839 -49.653  0.10 13.43           C  
+ATOM    129  O   SER L   1E    -22.829  36.818 -49.115  0.34 12.37           O  
+ATOM    161  N   CYS L   1     -27.779  33.791 -54.663  1.00 11.36           N  
+ATOM    162  CA  CYS L   1     -27.645  32.429 -54.138  1.00 11.72           C  
+ATOM    163  C   CYS L   1     -28.184  31.351 -55.065  1.00 12.46           C  
+ATOM    164  O   CYS L   1     -29.066  31.597 -55.887  1.00 11.13           O  
+ATOM    167  N   GLY L   2     -27.618  30.155 -54.931  1.00 11.94           N  
+ATOM    168  CA  GLY L   2     -28.093  29.010 -55.681  1.00 13.42           C  
+ATOM    169  C   GLY L   2     -27.920  28.936 -57.179  1.00 13.71           C  
+ATOM    170  O   GLY L   2     -28.452  28.010 -57.799  1.00 12.21           O  
+ATOM    171  N   LEU L   3     -27.207  29.893 -57.766  1.00 11.48           N  
+ATOM    172  CA  LEU L   3     -26.960  29.891 -59.207  1.00 12.60           C  
+ATOM    173  C   LEU L   3     -25.462  29.636 -59.346  1.00 13.82           C  
+ATOM    174  O   LEU L   3     -24.649  30.462 -58.944  1.00 14.29           O  
+TER     378      LEU L   3                                                      
+ATOM    498  N   MET H  32     -15.884  21.898 -46.134  0.03 13.63           N  
+ATOM    500  CA  MET H  32     -15.223  20.827 -45.399  0.10 13.62           C  
+ATOM    502  C   MET H  32     -14.910  21.331 -44.004  0.01 14.47           C  
+ATOM    504  O   MET H  32     -14.280  22.376 -43.844  0.10 14.26           O  
+ATOM    514  N   LEU H  33     -15.346  20.594 -42.992  1.00 15.12           N  
+ATOM    515  CA  LEU H  33     -15.057  20.994 -41.613  1.00 17.37           C  
+ATOM    516  C   LEU H  33     -13.966  20.110 -41.025  1.00 21.15           C  
+ATOM    517  O   LEU H  33     -14.053  18.878 -41.092  1.00 21.77           O  
+ATOM    544  N   LYS H  36      -8.375  20.177 -35.426  1.00 47.23           N  
+ATOM    545  CA  LYS H  36      -6.948  20.457 -35.546  1.00 49.79           C  
+ATOM    546  C   LYS H  36      -6.046  19.727 -34.564  1.00 51.19           C  
+ATOM    547  O   LYS H  36      -6.501  19.201 -33.546  1.00 51.77           O  
+ATOM    553  N   SER H  36A     -4.757  19.702 -34.898  0.40 52.14           N  
+ATOM    554  CA  SER H  36A     -3.731  19.057 -34.087  0.40 52.58           C  
+ATOM    555  C   SER H  36A     -4.254  17.826 -33.356  0.40 52.69           C  
+ATOM    556  O   SER H  36A     -4.508  17.868 -32.151  0.40 54.21           O  
+ATOM    553  N  BSER H  36A     -4.757  19.702 -34.898  0.60 52.14           N  
+ATOM    554  CA BSER H  36A     -3.731  19.057 -34.087  0.60 52.58           C  
+ATOM    555  C  BSER H  36A     -4.254  17.826 -33.356  0.60 52.69           C  
+ATOM    556  O  BSER H  36A     -4.508  17.868 -32.151  0.60 54.21           O  
+ATOM    583  N   LEU H  40     -10.561  15.413 -41.434  0.48 28.25           N  
+ATOM    585  CA  LEU H  40     -11.939  15.701 -41.811  0.03 25.33           C  
+ATOM    587  C   LEU H  40     -12.927  15.248 -40.743  0.13 23.56           C  
+ATOM    589  O   LEU H  40     -12.964  14.075 -40.371  0.11 23.23           O  
+ATOM    599  N   LEU H  41     -13.727  16.191 -40.255  0.44 21.23           N  
+ATOM    601  CA  LEU H  41     -14.727  15.903 -39.235  0.04 18.81           C  
+ATOM    603  C   LEU H  41     -16.114  15.742 -39.829  0.60 17.12           C  
+ATOM    605  O   LEU H  41     -16.804  14.756 -39.572  0.25 16.40           O  
+ATOM    615  N   CYS H  42     -16.515  16.722 -40.632  1.00 15.17           N  
+ATOM    616  CA  CYS H  42     -17.854  16.716 -41.198  1.00 14.43           C  
+ATOM    617  C   CYS H  42     -17.965  17.557 -42.446  1.00 13.79           C  
+ATOM    618  O   CYS H  42     -17.003  18.181 -42.892  1.00 13.66           O  
+ATOM    621  N   GLY H  43     -19.183  17.574 -42.976  1.00 12.50           N  
+ATOM    622  CA  GLY H  43     -19.506  18.388 -44.128  1.00 13.66           C  
+ATOM    623  C   GLY H  43     -20.155  19.637 -43.546  1.00 12.41           C  
+ATOM    624  O   GLY H  43     -20.400  19.711 -42.333  1.00 11.38           O  
+ATOM    625  N   ALA H  44     -20.433  20.608 -44.408  1.00 12.66           N  
+ATOM    626  CA  ALA H  44     -21.043  21.876 -44.015  1.00 12.16           C  
+ATOM    627  C   ALA H  44     -21.446  22.558 -45.312  1.00 11.20           C  
+ATOM    628  O   ALA H  44     -21.152  22.052 -46.394  1.00 11.04           O  
+TER     630      TER H  44
+CONECT 5572 5571
+MASTER      413    0   12   20   38    0    0    6 5736    3  109   55
+END
diff --git a/tests/data/altloc_3B9F_B.pdb b/tests/data/altloc_3B9F_B.pdb
new file mode 100644
index 0000000..c36b0e0
--- /dev/null
+++ b/tests/data/altloc_3B9F_B.pdb
@@ -0,0 +1,109 @@
+PDBTLS   This file was edited to test pdb_selaltloc
+PDBTLS   Original PDB 3B9F
+PDBTLS
+HEADER    HYDROLASE/HYDROLASE INHIBITOR           05-NOV-07   3B9F              
+TITLE     1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX                   
+COMPND  21 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+KEYWDS   4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX             
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    W.LI,T.E.ADAMS,J.A.HUNTINGTON                                         
+REVDAT   1   22-APR-08 3B9F    0                                                
+JRNL        AUTH   W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON           
+REMARK   2                                                                      
+REMARK 999 NATURAL VARIANT AT THIS POSITION                                     
+DBREF  3B9F I   17   387  UNP    P05154   IPSP_HUMAN      36    406             
+SEQADV 3B9F ALA H  195  UNP  P00734    SER   568 ENGINEERED MUTATION            
+SEQRES  31 I  395  LYS VAL ASN ARG PRO                                          
+MODRES 3B9F ASN H   60G ASN  GLYCOSYLATION SITE                                 
+HET    NAG  A   1      14                                                       
+HETNAM     NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE                         
+HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL                                    
+FORMUL  14  HOH   *523(H2 O)                                                    
+HELIX    1   1 ASN L    1K GLY L    1F 1                                   6    
+HELIX   20  20 SER I  305  THR I  309  5                                   5    
+SHEET    1   A 7 SER H  20  ASP H  21  0                                        
+SHEET    2   G 2 GLY I 340  ARG I 342  1  O  THR I 341   N  TRP I 190           
+SSBOND   1 CYS L    1    CYS H  122                          1555   1555  2.03  
+LINK         O6  NAG A   1                 C1  FUC A   2     1555   1555  1.40  
+CISPEP   2 LYS H  185    PRO H  186          0         0.28                     
+CRYST1   44.055   48.825   97.850  78.72  81.52  77.69 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.022699 -0.004951 -0.002582        0.00000                         
+SCALE2      0.000000  0.020963 -0.003616        0.00000                         
+SCALE3      0.000000  0.000000  0.010485        0.00000                         
+ATOM     16  N   TYR L   1P    -35.899  36.071 -57.146  1.00 24.40           N  
+ATOM     17  CA  TYR L   1P    -35.533  35.711 -55.782  1.00 22.98           C  
+ATOM     18  C   TYR L   1P    -35.689  36.923 -54.879  1.00 22.73           C  
+ATOM     19  O   TYR L   1P    -35.212  38.013 -55.199  1.00 24.86           O  
+ATOM     29  N   GLN L   1O    -36.368  36.734 -53.754  0.80 21.82           N  
+ATOM     31  CA  GLN L   1O    -36.567  37.813 -52.796  0.77 21.45           C  
+ATOM     33  C   GLN L   1O    -35.688  37.528 -51.586  0.65 20.57           C  
+ATOM     35  O   GLN L   1O    -35.820  36.482 -50.950  0.77 19.47           O  
+ATOM     46  N   THR L   1N    -34.783  38.453 -51.279  1.00 20.45           N  
+ATOM     47  CA  THR L   1N    -33.885  38.283 -50.143  1.00 20.33           C  
+ATOM     48  C   THR L   1N    -34.665  38.284 -48.834  1.00 20.94           C  
+ATOM     49  O   THR L   1N    -35.715  38.926 -48.718  1.00 20.47           O  
+ATOM    101  N   THR L   1H    -25.711  41.829 -41.231  1.00 16.46           N  
+ATOM    102  CA  THR L   1H    -25.418  40.733 -40.321  1.00 14.66           C  
+ATOM    103  C   THR L   1H    -25.179  39.417 -41.051  1.00 15.08           C  
+ATOM    104  O   THR L   1H    -24.467  38.557 -40.552  1.00 14.35           O  
+ATOM    124  N   SER L   1E    -22.558  39.094 -47.639  0.85 13.30           N  
+ATOM    126  CA  SER L   1E    -23.010  39.174 -49.023  0.84 12.40           C  
+ATOM    128  C   SER L   1E    -23.296  37.813 -49.635  0.82 12.51           C  
+ATOM    130  O   SER L   1E    -22.933  36.779 -49.072  0.42 11.68           O  
+ATOM    161  N   CYS L   1     -27.779  33.791 -54.663  1.00 11.36           N  
+ATOM    162  CA  CYS L   1     -27.645  32.429 -54.138  1.00 11.72           C  
+ATOM    163  C   CYS L   1     -28.184  31.351 -55.065  1.00 12.46           C  
+ATOM    164  O   CYS L   1     -29.066  31.597 -55.887  1.00 11.13           O  
+ATOM    167  N   GLY L   2     -27.618  30.155 -54.931  1.00 11.94           N  
+ATOM    168  CA  GLY L   2     -28.093  29.010 -55.681  1.00 13.42           C  
+ATOM    169  C   GLY L   2     -27.920  28.936 -57.179  1.00 13.71           C  
+ATOM    170  O   GLY L   2     -28.452  28.010 -57.799  1.00 12.21           O  
+ATOM    171  N   LEU L   3     -27.207  29.893 -57.766  1.00 11.48           N  
+ATOM    172  CA  LEU L   3     -26.960  29.891 -59.207  1.00 12.60           C  
+ATOM    173  C   LEU L   3     -25.462  29.636 -59.346  1.00 13.82           C  
+ATOM    174  O   LEU L   3     -24.649  30.462 -58.944  1.00 14.29           O  
+TER     378      LEU L   3                                                      
+ATOM    499  N   MET H  32     -15.886  21.863 -46.147  0.84 13.45           N  
+ATOM    501  CA  MET H  32     -15.262  20.752 -45.438  0.90 14.92           C  
+ATOM    503  C   MET H  32     -14.862  21.255 -44.046  0.99 15.40           C  
+ATOM    505  O   MET H  32     -14.125  22.236 -43.935  0.67 14.61           O  
+ATOM    514  N   LEU H  33     -15.346  20.594 -42.992  1.00 15.12           N  
+ATOM    515  CA  LEU H  33     -15.057  20.994 -41.613  1.00 17.37           C  
+ATOM    516  C   LEU H  33     -13.966  20.110 -41.025  1.00 21.15           C  
+ATOM    517  O   LEU H  33     -14.053  18.878 -41.092  1.00 21.77           O  
+ATOM    544  N   LYS H  36      -8.375  20.177 -35.426  1.00 47.23           N  
+ATOM    545  CA  LYS H  36      -6.948  20.457 -35.546  1.00 49.79           C  
+ATOM    546  C   LYS H  36      -6.046  19.727 -34.564  1.00 51.19           C  
+ATOM    547  O   LYS H  36      -6.501  19.201 -33.546  1.00 51.77           O  
+ATOM    553  N   SER H  36A     -4.757  19.702 -34.898  0.60 52.14           N  
+ATOM    554  CA  SER H  36A     -3.731  19.057 -34.087  0.60 52.58           C  
+ATOM    555  C   SER H  36A     -4.254  17.826 -33.356  0.60 52.69           C  
+ATOM    556  O   SER H  36A     -4.508  17.868 -32.151  0.60 54.21           O  
+ATOM    584  N   LEU H  40     -10.564  15.370 -41.413  0.48 28.64           N  
+ATOM    586  CA  LEU H  40     -11.952  15.605 -41.789  0.97 26.04           C  
+ATOM    588  C   LEU H  40     -12.860  15.301 -40.605  0.61 24.27           C  
+ATOM    590  O   LEU H  40     -12.739  14.255 -39.969  0.89 22.89           O  
+ATOM    600  N   LEU H  41     -13.774  16.219 -40.316  0.53 22.16           N  
+ATOM    602  CA  LEU H  41     -14.696  16.049 -39.204  0.96 19.96           C  
+ATOM    604  C   LEU H  41     -16.124  15.865 -39.697  0.40 18.03           C  
+ATOM    606  O   LEU H  41     -16.844  14.976 -39.247  0.61 16.77           O  
+ATOM    615  N   CYS H  42     -16.515  16.722 -40.632  1.00 15.17           N  
+ATOM    616  CA  CYS H  42     -17.854  16.716 -41.198  1.00 14.43           C  
+ATOM    617  C   CYS H  42     -17.965  17.557 -42.446  1.00 13.79           C  
+ATOM    618  O   CYS H  42     -17.003  18.181 -42.892  1.00 13.66           O  
+ATOM    621  N   GLY H  43     -19.183  17.574 -42.976  1.00 12.50           N  
+ATOM    622  CA  GLY H  43     -19.506  18.388 -44.128  1.00 13.66           C  
+ATOM    623  C   GLY H  43     -20.155  19.637 -43.546  1.00 12.41           C  
+ATOM    624  O   GLY H  43     -20.400  19.711 -42.333  1.00 11.38           O  
+ATOM    625  N   ALA H  44     -20.433  20.608 -44.408  1.00 12.66           N  
+ATOM    626  CA  ALA H  44     -21.043  21.876 -44.015  1.00 12.16           C  
+ATOM    627  C   ALA H  44     -21.446  22.558 -45.312  1.00 11.20           C  
+ATOM    628  O   ALA H  44     -21.152  22.052 -46.394  1.00 11.04           O  
+TER     630      TER H  44
+CONECT 5572 5571
+MASTER      413    0   12   20   38    0    0    6 5736    3  109   55
+END
diff --git a/tests/data/altloc_3B9F_nooption.pdb b/tests/data/altloc_3B9F_nooption.pdb
new file mode 100644
index 0000000..6c98e5d
--- /dev/null
+++ b/tests/data/altloc_3B9F_nooption.pdb
@@ -0,0 +1,109 @@
+PDBTLS   This file was edited to test pdb_selaltloc
+PDBTLS   Original PDB 3B9F
+PDBTLS
+HEADER    HYDROLASE/HYDROLASE INHIBITOR           05-NOV-07   3B9F              
+TITLE     1.6 A STRUCTURE OF THE PCI-THROMBIN-HEPARIN COMPLEX                   
+COMPND  21 ENGINEERED: YES                                                      
+SOURCE    MOL_ID: 1;                                                            
+KEYWDS   4 PROTEASE, ZYMOGEN, HYDROLASE-HYDROLASE INHIBITOR COMPLEX             
+EXPDTA    X-RAY DIFFRACTION                                                     
+AUTHOR    W.LI,T.E.ADAMS,J.A.HUNTINGTON                                         
+REVDAT   1   22-APR-08 3B9F    0                                                
+JRNL        AUTH   W.LI,T.E.ADAMS,J.NANGALIA,C.T.ESMON,J.A.HUNTINGTON           
+REMARK   2                                                                      
+REMARK 999 NATURAL VARIANT AT THIS POSITION                                     
+DBREF  3B9F I   17   387  UNP    P05154   IPSP_HUMAN      36    406             
+SEQADV 3B9F ALA H  195  UNP  P00734    SER   568 ENGINEERED MUTATION            
+SEQRES  31 I  395  LYS VAL ASN ARG PRO                                          
+MODRES 3B9F ASN H   60G ASN  GLYCOSYLATION SITE                                 
+HET    NAG  A   1      14                                                       
+HETNAM     NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE                         
+HETSYN     GOL GLYCERIN; PROPANE-1,2,3-TRIOL                                    
+FORMUL  14  HOH   *523(H2 O)                                                    
+HELIX    1   1 ASN L    1K GLY L    1F 1                                   6    
+HELIX   20  20 SER I  305  THR I  309  5                                   5    
+SHEET    1   A 7 SER H  20  ASP H  21  0                                        
+SHEET    2   G 2 GLY I 340  ARG I 342  1  O  THR I 341   N  TRP I 190           
+SSBOND   1 CYS L    1    CYS H  122                          1555   1555  2.03  
+LINK         O6  NAG A   1                 C1  FUC A   2     1555   1555  1.40  
+CISPEP   2 LYS H  185    PRO H  186          0         0.28                     
+CRYST1   44.055   48.825   97.850  78.72  81.52  77.69 P 1           1          
+ORIGX1      1.000000  0.000000  0.000000        0.00000                         
+ORIGX2      0.000000  1.000000  0.000000        0.00000                         
+ORIGX3      0.000000  0.000000  1.000000        0.00000                         
+SCALE1      0.022699 -0.004951 -0.002582        0.00000                         
+SCALE2      0.000000  0.020963 -0.003616        0.00000                         
+SCALE3      0.000000  0.000000  0.010485        0.00000                         
+ATOM     16  N   TYR L   1P    -35.899  36.071 -57.146  1.00 24.40           N  
+ATOM     17  CA  TYR L   1P    -35.533  35.711 -55.782  1.00 22.98           C  
+ATOM     18  C   TYR L   1P    -35.689  36.923 -54.879  1.00 22.73           C  
+ATOM     19  O   TYR L   1P    -35.212  38.013 -55.199  1.00 24.86           O  
+ATOM     29  N   GLN L   1O    -36.368  36.734 -53.754  0.80 21.82           N  
+ATOM     31  CA  GLN L   1O    -36.567  37.813 -52.796  0.77 21.45           C  
+ATOM     33  C   GLN L   1O    -35.688  37.528 -51.586  0.65 20.57           C  
+ATOM     35  O   GLN L   1O    -35.820  36.482 -50.950  0.77 19.47           O  
+ATOM     46  N   THR L   1N    -34.783  38.453 -51.279  1.00 20.45           N  
+ATOM     47  CA  THR L   1N    -33.885  38.283 -50.143  1.00 20.33           C  
+ATOM     48  C   THR L   1N    -34.665  38.284 -48.834  1.00 20.94           C  
+ATOM     49  O   THR L   1N    -35.715  38.926 -48.718  1.00 20.47           O  
+ATOM    101  N   THR L   1H    -25.711  41.829 -41.231  1.00 16.46           N  
+ATOM    102  CA  THR L   1H    -25.418  40.733 -40.321  1.00 14.66           C  
+ATOM    103  C   THR L   1H    -25.179  39.417 -41.051  1.00 15.08           C  
+ATOM    104  O   THR L   1H    -24.467  38.557 -40.552  1.00 14.35           O  
+ATOM    124  N   SER L   1E    -22.558  39.094 -47.639  0.85 13.30           N  
+ATOM    126  CA  SER L   1E    -23.010  39.174 -49.023  0.84 12.40           C  
+ATOM    128  C   SER L   1E    -23.296  37.813 -49.635  0.82 12.51           C  
+ATOM    130  O   SER L   1E    -22.933  36.779 -49.072  0.42 11.68           O  
+ATOM    161  N   CYS L   1     -27.779  33.791 -54.663  1.00 11.36           N  
+ATOM    162  CA  CYS L   1     -27.645  32.429 -54.138  1.00 11.72           C  
+ATOM    163  C   CYS L   1     -28.184  31.351 -55.065  1.00 12.46           C  
+ATOM    164  O   CYS L   1     -29.066  31.597 -55.887  1.00 11.13           O  
+ATOM    167  N   GLY L   2     -27.618  30.155 -54.931  1.00 11.94           N  
+ATOM    168  CA  GLY L   2     -28.093  29.010 -55.681  1.00 13.42           C  
+ATOM    169  C   GLY L   2     -27.920  28.936 -57.179  1.00 13.71           C  
+ATOM    170  O   GLY L   2     -28.452  28.010 -57.799  1.00 12.21           O  
+ATOM    171  N   LEU L   3     -27.207  29.893 -57.766  1.00 11.48           N  
+ATOM    172  CA  LEU L   3     -26.960  29.891 -59.207  1.00 12.60           C  
+ATOM    173  C   LEU L   3     -25.462  29.636 -59.346  1.00 13.82           C  
+ATOM    174  O   LEU L   3     -24.649  30.462 -58.944  1.00 14.29           O  
+TER     378      LEU L   3                                                      
+ATOM    499  N   MET H  32     -15.886  21.863 -46.147  0.84 13.45           N  
+ATOM    501  CA  MET H  32     -15.262  20.752 -45.438  0.90 14.92           C  
+ATOM    503  C   MET H  32     -14.862  21.255 -44.046  0.99 15.40           C  
+ATOM    505  O   MET H  32     -14.125  22.236 -43.935  0.67 14.61           O  
+ATOM    514  N   LEU H  33     -15.346  20.594 -42.992  1.00 15.12           N  
+ATOM    515  CA  LEU H  33     -15.057  20.994 -41.613  1.00 17.37           C  
+ATOM    516  C   LEU H  33     -13.966  20.110 -41.025  1.00 21.15           C  
+ATOM    517  O   LEU H  33     -14.053  18.878 -41.092  1.00 21.77           O  
+ATOM    544  N   LYS H  36      -8.375  20.177 -35.426  1.00 47.23           N  
+ATOM    545  CA  LYS H  36      -6.948  20.457 -35.546  1.00 49.79           C  
+ATOM    546  C   LYS H  36      -6.046  19.727 -34.564  1.00 51.19           C  
+ATOM    547  O   LYS H  36      -6.501  19.201 -33.546  1.00 51.77           O  
+ATOM    553  N   SER H  36A     -4.757  19.702 -34.898  0.60 52.14           N  
+ATOM    554  CA  SER H  36A     -3.731  19.057 -34.087  0.60 52.58           C  
+ATOM    555  C   SER H  36A     -4.254  17.826 -33.356  0.60 52.69           C  
+ATOM    556  O   SER H  36A     -4.508  17.868 -32.151  0.60 54.21           O  
+ATOM    583  N   LEU H  40     -10.561  15.413 -41.434  0.48 28.25           N  
+ATOM    586  CA  LEU H  40     -11.952  15.605 -41.789  0.97 26.04           C  
+ATOM    588  C   LEU H  40     -12.860  15.301 -40.605  0.61 24.27           C  
+ATOM    590  O   LEU H  40     -12.739  14.255 -39.969  0.89 22.89           O  
+ATOM    600  N   LEU H  41     -13.774  16.219 -40.316  0.53 22.16           N  
+ATOM    602  CA  LEU H  41     -14.696  16.049 -39.204  0.96 19.96           C  
+ATOM    603  C   LEU H  41     -16.114  15.742 -39.829  0.60 17.12           C  
+ATOM    606  O   LEU H  41     -16.844  14.976 -39.247  0.61 16.77           O  
+ATOM    615  N   CYS H  42     -16.515  16.722 -40.632  1.00 15.17           N  
+ATOM    616  CA  CYS H  42     -17.854  16.716 -41.198  1.00 14.43           C  
+ATOM    617  C   CYS H  42     -17.965  17.557 -42.446  1.00 13.79           C  
+ATOM    618  O   CYS H  42     -17.003  18.181 -42.892  1.00 13.66           O  
+ATOM    621  N   GLY H  43     -19.183  17.574 -42.976  1.00 12.50           N  
+ATOM    622  CA  GLY H  43     -19.506  18.388 -44.128  1.00 13.66           C  
+ATOM    623  C   GLY H  43     -20.155  19.637 -43.546  1.00 12.41           C  
+ATOM    624  O   GLY H  43     -20.400  19.711 -42.333  1.00 11.38           O  
+ATOM    625  N   ALA H  44     -20.433  20.608 -44.408  1.00 12.66           N  
+ATOM    626  CA  ALA H  44     -21.043  21.876 -44.015  1.00 12.16           C  
+ATOM    627  C   ALA H  44     -21.446  22.558 -45.312  1.00 11.20           C  
+ATOM    628  O   ALA H  44     -21.152  22.052 -46.394  1.00 11.04           O  
+TER     630      TER H  44
+CONECT 5572 5571
+MASTER      413    0   12   20   38    0    0    6 5736    3  109   55
+END
diff --git a/tests/data/dummy_altloc.pdb b/tests/data/dummy_altloc.pdb
index c207e46..f692ff5 100644
--- a/tests/data/dummy_altloc.pdb
+++ b/tests/data/dummy_altloc.pdb
@@ -7,6 +7,9 @@ ATOM    310  C  ASER A  22     -12.365  -3.540 -14.113  0.53  4.77           C
 ANISOU  310  C  ASER A  22      582    560    669     34     31     98       C  
 ATOM    311  O  ASER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
 ANISOU  311  O  ASER A  22      602    786    679     59     46    138       O  
+REMARK  This is a crazy remark in the middle of the file
+REMARK  which must appear in the same place after pdb_selaltloc,
+REMARK  that is, after the SER and before the PRO
 ATOM    318  N  BPRO A  22     -14.305  -3.040 -15.563  0.47  5.18           N  
 ANISOU  318  N  BPRO A  22      713    566    690    -20    -45      8       N  
 ATOM    319  CA BPRO A  22     -13.801  -3.851 -14.452  0.47  5.29           C  
diff --git a/tests/data/dummy_altloc4.pdb b/tests/data/dummy_altloc4.pdb
new file mode 100644
index 0000000..f4e29cb
--- /dev/null
+++ b/tests/data/dummy_altloc4.pdb
@@ -0,0 +1,35 @@
+ATOM    153  N   VAL A  18      -0.264 -17.574  22.788  0.00  0.00           N  
+ATOM    154  CA  VAL A  18      -0.201 -17.901  24.209  0.00  0.00           C  
+ATOM    155  C   VAL A  18      -1.047 -19.150  24.437  0.00  0.00           C  
+ATOM    156  O   VAL A  18      -2.260 -19.144  24.214  0.00  0.00           O  
+ATOM    157  CB  VAL A  18      -0.689 -16.724  25.084  0.00  0.00           C  
+ATOM    161  N   TRP A  19      -0.408 -20.230  24.882  0.00  0.00           N  
+ATOM    162  CA  TRP A  19      -1.091 -21.490  25.161  0.00  0.00           C  
+ATOM    163  C   TRP A  19      -1.303 -21.563  26.667  0.00  0.00           C  
+ATOM    164  O   TRP A  19      -0.357 -21.920  27.375  0.00  0.00           O  
+ATOM    165  CB  TRP A  19      -0.272 -22.670  24.635  0.00  0.00           C  
+ATOM    176  N   TYR A  20      -2.522 -21.226  27.083  0.00  0.00           N  
+ATOM    177  CA  TYR A  20      -2.898 -21.178  28.493  0.00  0.00           C  
+ATOM    178  C   TYR A  20      -3.718 -22.410  28.851  0.00  0.00           C  
+ATOM    179  O   TYR A  20      -4.629 -22.780  28.105  0.00  0.00           O  
+ATOM    180  CB  TYR A  20      -3.681 -19.898  28.795  0.00  0.00           C  
+ATOM    189  N  AVAL A  21      -3.396 -23.034  29.982  0.50  0.00           N  
+ATOM    197  N  BALA A  21      -5.676 -24.647  32.284  0.50  0.00           N  
+ATOM    190  CA AVAL A  21      -4.121 -24.205  30.467  0.50  0.00           C  
+ATOM    198  CA BALA A  21      -6.012 -24.814  33.696  0.50  0.00           C  
+ATOM    191  C  AVAL A  21      -4.530 -24.072  31.930  0.50  0.00           C  
+ATOM    199  C  BALA A  21      -4.990 -25.677  34.426  0.50  0.00           C  
+ATOM    192  O  AVAL A  21      -3.835 -23.461  32.747  0.50  0.00           O  
+ATOM    200  O  BALA A  21      -4.494 -26.675  33.897  0.50  0.00           O  
+ATOM    193  CB AVAL A  21      -3.289 -25.497  30.298  0.50  0.00           C  
+ATOM    201  CB BALA A  21      -7.405 -25.428  33.847  0.50  0.00           C  
+ATOM    189  N  APRO A  22      -3.396 -23.034  29.982  0.50  0.00           N  
+ATOM    190  CA APRO A  22      -4.121 -24.205  30.467  0.50  0.00           C  
+ATOM    191  C  APRO A  22      -4.530 -24.072  31.930  0.50  0.00           C  
+ATOM    192  O  APRO A  22      -3.835 -23.461  32.747  0.50  0.00           O  
+ATOM    193  CB APRO A  22      -3.289 -25.497  30.298  0.50  0.00           C  
+ATOM    197  N  BGLY A  22      -5.676 -24.647  32.284  0.50  0.00           N  
+ATOM    198  CA BGLY A  22      -6.012 -24.814  33.696  0.50  0.00           C  
+ATOM    199  C  BGLY A  22      -4.990 -25.677  34.426  0.50  0.00           C  
+ATOM    200  O  BGLY A  22      -4.494 -26.675  33.897  0.50  0.00           O  
+ATOM    201  CB BGLY A  22      -7.405 -25.428  33.847  0.50  0.00           C  
diff --git a/tests/data/dummy_altloc_chains.pdb b/tests/data/dummy_altloc_chains.pdb
new file mode 100644
index 0000000..97d3ab9
--- /dev/null
+++ b/tests/data/dummy_altloc_chains.pdb
@@ -0,0 +1,54 @@
+REMARK ORIGINAL DATA FROM PDB ID 3U7T
+ATOM      1  N  ASER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU    1  N  ASER A  22      594    482    661      7    -42     32       N  
+ATOM      2  CA ASER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU    2  CA ASER A  22      695    586    731      6    -19    117       C  
+ATOM      3  C  ASER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU    3  C  ASER A  22      582    560    669     34     31     98       C  
+ATOM      4  O  ASER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU    4  O  ASER A  22      602    786    679     59     46    138       O  
+ATOM      5  N  BPRO A  22     -14.305  -3.040 -15.563  0.47  5.18           N  
+ANISOU    5  N  BPRO A  22      713    566    690    -20    -45      8       N  
+ATOM      6  CA BPRO A  22     -13.801  -3.851 -14.452  0.47  5.29           C  
+ANISOU    6  CA BPRO A  22      701    599    711    -19    -20     59       C  
+ATOM      7  C  BPRO A  22     -12.344  -3.583 -14.119  0.47  4.84           C  
+ANISOU    7  C  BPRO A  22      590    585    664     23     27     64       C  
+ATOM      8  O  BPRO A  22     -11.499  -3.414 -15.007  0.47  5.37           O  
+ANISOU    8  O  BPRO A  22      603    762    675     65     45    100       O  
+ATOM      9  N  CGLU B  22     -12.046  -3.614 -12.827  0.30  4.76           N  
+ANISOU    9  N  CGLU B  22      558    607    642     79     39     69       N  
+ATOM     10  CA CGLU B  22     -10.679  -3.437 -12.387  0.30  4.89           C  
+ANISOU   10  CA CGLU B  22      576    620    663     31     42     45       C  
+ATOM     11  C  CGLU B  22      -9.718  -4.412 -13.075  0.30  4.66           C  
+ANISOU   11  C  CGLU B  22      509    598    663      8     21     49       C  
+ATOM     12  O  CGLU B  22      -8.593  -4.031 -13.405  0.30  5.42           O  
+ANISOU   12  O  CGLU B  22      569    765    725    -40     72    -21       O  
+ATOM     13  N  DALA B  22     -10.141  -5.661 -13.285  0.70  4.86           N  
+ANISOU   13  N  DALA B  22      551    614    679     31     34     65       N  
+ATOM     14  CA DALA B  22      -9.236  -6.655 -13.860  0.70  5.12           C  
+ANISOU   14  CA DALA B  22      659    547    738     54     48     91       C  
+ATOM     15  C  DALA B  22      -8.797  -6.289 -15.284  0.70  4.57           C  
+ANISOU   15  C  DALA B  22      574    482    682     38    -18     30       C  
+ATOM     16  O  DALA B  22      -7.651  -6.544 -15.670  0.70  5.51           O  
+ANISOU   16  O  DALA B  22      643    726    724    126     19     56       O  
+ATOM     17  N   ILE B  23      -9.702  -5.727 -16.084  0.01  4.36           N  
+ANISOU   17  N   ILE B  23      520    465    672     33    -18      2       N  
+ATOM     18  CA  ILE B  23      -9.340  -5.286 -17.428  0.01  4.45           C  
+ANISOU   18  CA  ILE B  23      533    529    630     -6    -50     -5       C  
+ATOM     19  C   ILE B  23      -8.471  -4.014 -17.377  0.01  4.39           C  
+ANISOU   19  C   ILE B  23      478    580    609     -1    -12    -14       C  
+ATOM     20  O   ILE B  23      -7.519  -3.868 -18.141  0.01  5.13           O  
+ANISOU   20  O   ILE B  23      566    725    660    -65     86    -77       O  
+ATOM     21  N  ALEU B  23      -9.706  -5.722 -16.071  0.99  4.68           N  
+ANISOU   21  N  ALEU B  23      553    548    676     10    -26     -1       N  
+ATOM     22  CA ALEU B  23      -9.351  -5.281 -17.410  0.99  4.87           C  
+ANISOU   22  CA ALEU B  23      554    645    651    -35    -48    -28       C  
+ATOM     23  C  ALEU B  23      -8.459  -4.039 -17.346  0.99  4.69           C  
+ANISOU   23  C  ALEU B  23      518    645    621    -13    -18    -33       C  
+ATOM     24  O  ALEU B  23      -7.460  -3.953 -18.055  0.99  5.25           O  
+ANISOU   24  O  ALEU B  23      583    759    652    -28     45    -75       O  
+ATOM     25  CA AGLU B  24     -10.000  -3.000 -12.000  0.45  4.89           C  
+ANISOU   25  CA AGLU B  24      576    620    663     31     42     45       C  
+ATOM     26  CA CGLU B  24     -10.679  -3.437 -12.387  0.55  4.89           C  
+ANISOU   26  CA CGLU B  24      576    620    663     31     42     45       C  
+END
diff --git a/tests/data/dummy_altloc_chains_A.pdb b/tests/data/dummy_altloc_chains_A.pdb
new file mode 100644
index 0000000..cf5b49d
--- /dev/null
+++ b/tests/data/dummy_altloc_chains_A.pdb
@@ -0,0 +1,36 @@
+REMARK ORIGINAL DATA FROM PDB ID 3U7T
+ATOM      1  N   SER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU    1  N   SER A  22      594    482    661      7    -42     32       N  
+ATOM      2  CA  SER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU    2  CA  SER A  22      695    586    731      6    -19    117       C  
+ATOM      3  C   SER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU    3  C   SER A  22      582    560    669     34     31     98       C  
+ATOM      4  O   SER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU    4  O   SER A  22      602    786    679     59     46    138       O  
+ATOM      9  N  CGLU B  22     -12.046  -3.614 -12.827  0.30  4.76           N  
+ANISOU    9  N  CGLU B  22      558    607    642     79     39     69       N  
+ATOM     10  CA CGLU B  22     -10.679  -3.437 -12.387  0.30  4.89           C  
+ANISOU   10  CA CGLU B  22      576    620    663     31     42     45       C  
+ATOM     11  C  CGLU B  22      -9.718  -4.412 -13.075  0.30  4.66           C  
+ANISOU   11  C  CGLU B  22      509    598    663      8     21     49       C  
+ATOM     12  O  CGLU B  22      -8.593  -4.031 -13.405  0.30  5.42           O  
+ANISOU   12  O  CGLU B  22      569    765    725    -40     72    -21       O  
+ATOM     13  N  DALA B  22     -10.141  -5.661 -13.285  0.70  4.86           N  
+ANISOU   13  N  DALA B  22      551    614    679     31     34     65       N  
+ATOM     14  CA DALA B  22      -9.236  -6.655 -13.860  0.70  5.12           C  
+ANISOU   14  CA DALA B  22      659    547    738     54     48     91       C  
+ATOM     15  C  DALA B  22      -8.797  -6.289 -15.284  0.70  4.57           C  
+ANISOU   15  C  DALA B  22      574    482    682     38    -18     30       C  
+ATOM     16  O  DALA B  22      -7.651  -6.544 -15.670  0.70  5.51           O  
+ANISOU   16  O  DALA B  22      643    726    724    126     19     56       O  
+ATOM     21  N   LEU B  23      -9.706  -5.722 -16.071  0.99  4.68           N  
+ANISOU   21  N   LEU B  23      553    548    676     10    -26     -1       N  
+ATOM     22  CA  LEU B  23      -9.351  -5.281 -17.410  0.99  4.87           C  
+ANISOU   22  CA  LEU B  23      554    645    651    -35    -48    -28       C  
+ATOM     23  C   LEU B  23      -8.459  -4.039 -17.346  0.99  4.69           C  
+ANISOU   23  C   LEU B  23      518    645    621    -13    -18    -33       C  
+ATOM     24  O   LEU B  23      -7.460  -3.953 -18.055  0.99  5.25           O  
+ANISOU   24  O   LEU B  23      583    759    652    -28     45    -75       O  
+ATOM     25  CA  GLU B  24     -10.000  -3.000 -12.000  0.45  4.89           C  
+ANISOU   25  CA  GLU B  24      576    620    663     31     42     45       C  
+END
diff --git a/tests/data/dummy_altloc_chains_C.pdb b/tests/data/dummy_altloc_chains_C.pdb
new file mode 100644
index 0000000..2ca99fa
--- /dev/null
+++ b/tests/data/dummy_altloc_chains_C.pdb
@@ -0,0 +1,44 @@
+REMARK ORIGINAL DATA FROM PDB ID 3U7T
+ATOM      1  N  ASER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU    1  N  ASER A  22      594    482    661      7    -42     32       N  
+ATOM      2  CA ASER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU    2  CA ASER A  22      695    586    731      6    -19    117       C  
+ATOM      3  C  ASER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU    3  C  ASER A  22      582    560    669     34     31     98       C  
+ATOM      4  O  ASER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU    4  O  ASER A  22      602    786    679     59     46    138       O  
+ATOM      5  N  BPRO A  22     -14.305  -3.040 -15.563  0.47  5.18           N  
+ANISOU    5  N  BPRO A  22      713    566    690    -20    -45      8       N  
+ATOM      6  CA BPRO A  22     -13.801  -3.851 -14.452  0.47  5.29           C  
+ANISOU    6  CA BPRO A  22      701    599    711    -19    -20     59       C  
+ATOM      7  C  BPRO A  22     -12.344  -3.583 -14.119  0.47  4.84           C  
+ANISOU    7  C  BPRO A  22      590    585    664     23     27     64       C  
+ATOM      8  O  BPRO A  22     -11.499  -3.414 -15.007  0.47  5.37           O  
+ANISOU    8  O  BPRO A  22      603    762    675     65     45    100       O  
+ATOM      9  N   GLU B  22     -12.046  -3.614 -12.827  0.30  4.76           N  
+ANISOU    9  N   GLU B  22      558    607    642     79     39     69       N  
+ATOM     10  CA  GLU B  22     -10.679  -3.437 -12.387  0.30  4.89           C  
+ANISOU   10  CA  GLU B  22      576    620    663     31     42     45       C  
+ATOM     11  C   GLU B  22      -9.718  -4.412 -13.075  0.30  4.66           C  
+ANISOU   11  C   GLU B  22      509    598    663      8     21     49       C  
+ATOM     12  O   GLU B  22      -8.593  -4.031 -13.405  0.30  5.42           O  
+ANISOU   12  O   GLU B  22      569    765    725    -40     72    -21       O  
+ATOM     17  N   ILE B  23      -9.702  -5.727 -16.084  0.01  4.36           N  
+ANISOU   17  N   ILE B  23      520    465    672     33    -18      2       N  
+ATOM     18  CA  ILE B  23      -9.340  -5.286 -17.428  0.01  4.45           C  
+ANISOU   18  CA  ILE B  23      533    529    630     -6    -50     -5       C  
+ATOM     19  C   ILE B  23      -8.471  -4.014 -17.377  0.01  4.39           C  
+ANISOU   19  C   ILE B  23      478    580    609     -1    -12    -14       C  
+ATOM     20  O   ILE B  23      -7.519  -3.868 -18.141  0.01  5.13           O  
+ANISOU   20  O   ILE B  23      566    725    660    -65     86    -77       O  
+ATOM     21  N  ALEU B  23      -9.706  -5.722 -16.071  0.99  4.68           N  
+ANISOU   21  N  ALEU B  23      553    548    676     10    -26     -1       N  
+ATOM     22  CA ALEU B  23      -9.351  -5.281 -17.410  0.99  4.87           C  
+ANISOU   22  CA ALEU B  23      554    645    651    -35    -48    -28       C  
+ATOM     23  C  ALEU B  23      -8.459  -4.039 -17.346  0.99  4.69           C  
+ANISOU   23  C  ALEU B  23      518    645    621    -13    -18    -33       C  
+ATOM     24  O  ALEU B  23      -7.460  -3.953 -18.055  0.99  5.25           O  
+ANISOU   24  O  ALEU B  23      583    759    652    -28     45    -75       O  
+ATOM     26  CA  GLU B  24     -10.679  -3.437 -12.387  0.55  4.89           C  
+ANISOU   26  CA  GLU B  24      576    620    663     31     42     45       C  
+END
diff --git a/tests/data/dummy_altloc_chains_maxocc.pdb b/tests/data/dummy_altloc_chains_maxocc.pdb
new file mode 100644
index 0000000..a667a64
--- /dev/null
+++ b/tests/data/dummy_altloc_chains_maxocc.pdb
@@ -0,0 +1,28 @@
+REMARK ORIGINAL DATA FROM PDB ID 3U7T
+ATOM      1  N   SER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU    1  N   SER A  22      594    482    661      7    -42     32       N  
+ATOM      2  CA  SER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU    2  CA  SER A  22      695    586    731      6    -19    117       C  
+ATOM      3  C   SER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU    3  C   SER A  22      582    560    669     34     31     98       C  
+ATOM      4  O   SER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU    4  O   SER A  22      602    786    679     59     46    138       O  
+ATOM     13  N   ALA B  22     -10.141  -5.661 -13.285  0.70  4.86           N  
+ANISOU   13  N   ALA B  22      551    614    679     31     34     65       N  
+ATOM     14  CA  ALA B  22      -9.236  -6.655 -13.860  0.70  5.12           C  
+ANISOU   14  CA  ALA B  22      659    547    738     54     48     91       C  
+ATOM     15  C   ALA B  22      -8.797  -6.289 -15.284  0.70  4.57           C  
+ANISOU   15  C   ALA B  22      574    482    682     38    -18     30       C  
+ATOM     16  O   ALA B  22      -7.651  -6.544 -15.670  0.70  5.51           O  
+ANISOU   16  O   ALA B  22      643    726    724    126     19     56       O  
+ATOM     21  N   LEU B  23      -9.706  -5.722 -16.071  0.99  4.68           N  
+ANISOU   21  N   LEU B  23      553    548    676     10    -26     -1       N  
+ATOM     22  CA  LEU B  23      -9.351  -5.281 -17.410  0.99  4.87           C  
+ANISOU   22  CA  LEU B  23      554    645    651    -35    -48    -28       C  
+ATOM     23  C   LEU B  23      -8.459  -4.039 -17.346  0.99  4.69           C  
+ANISOU   23  C   LEU B  23      518    645    621    -13    -18    -33       C  
+ATOM     24  O   LEU B  23      -7.460  -3.953 -18.055  0.99  5.25           O  
+ANISOU   24  O   LEU B  23      583    759    652    -28     45    -75       O  
+ATOM     26  CA  GLU B  24     -10.679  -3.437 -12.387  0.55  4.89           C  
+ANISOU   26  CA  GLU B  24      576    620    663     31     42     45       C  
+END
diff --git a/tests/data/dummy_altloc_model.pdb b/tests/data/dummy_altloc_model.pdb
new file mode 100644
index 0000000..fb30010
--- /dev/null
+++ b/tests/data/dummy_altloc_model.pdb
@@ -0,0 +1,55 @@
+REMARK ORIGINAL DATA FROM PDB ID 3U7T                                           
+REMARK test MODEL without the TER ENDMDL or END statements                      
+MODEL        1                                                                  
+ATOM    308  N  ASER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU  308  N  ASER A  22      594    482    661      7    -42     32       N  
+ATOM    309  CA ASER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU  309  CA ASER A  22      695    586    731      6    -19    117       C  
+ATOM    310  C  ASER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU  310  C  ASER A  22      582    560    669     34     31     98       C  
+ATOM    311  O  ASER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU  311  O  ASER A  22      602    786    679     59     46    138       O  
+ATOM    318  N  BPRO A  22     -14.305  -3.040 -15.563  0.47  5.18           N  
+ANISOU  318  N  BPRO A  22      713    566    690    -20    -45      8       N  
+ATOM    319  CA BPRO A  22     -13.801  -3.851 -14.452  0.47  5.29           C  
+ANISOU  319  CA BPRO A  22      701    599    711    -19    -20     59       C  
+ATOM    320  C  BPRO A  22     -12.344  -3.583 -14.119  0.47  4.84           C  
+ANISOU  320  C  BPRO A  22      590    585    664     23     27     64       C  
+ATOM    321  O  BPRO A  22     -11.499  -3.414 -15.007  0.47  5.37           O  
+ANISOU  321  O  BPRO A  22      603    762    675     65     45    100       O  
+ATOM    332  N   GLU A  23     -12.046  -3.614 -12.827  1.00  4.76           N  
+ANISOU  332  N   GLU A  23      558    607    642     79     39     69       N  
+ATOM    333  CA  GLU A  23     -10.679  -3.437 -12.387  1.00  4.89           C  
+ANISOU  333  CA  GLU A  23      576    620    663     31     42     45       C  
+ATOM    334  C   GLU A  23      -9.718  -4.412 -13.075  1.00  4.66           C  
+ANISOU  334  C   GLU A  23      509    598    663      8     21     49       C  
+ATOM    335  O   GLU A  23      -8.593  -4.031 -13.405  1.00  5.42           O  
+ANISOU  335  O   GLU A  23      569    765    725    -40     72    -21       O  
+MODEL        2                                                                  
+ATOM    308  N  ASER A  22     -14.282  -3.023 -15.571  0.53  4.57           N  
+ANISOU  308  N  ASER A  22      594    482    661      7    -42     32       N  
+ATOM    309  CA ASER A  22     -13.829  -3.816 -14.436  0.53  5.30           C  
+ANISOU  309  CA ASER A  22      695    586    731      6    -19    117       C  
+ATOM    310  C  ASER A  22     -12.365  -3.540 -14.113  0.53  4.77           C  
+ANISOU  310  C  ASER A  22      582    560    669     34     31     98       C  
+ATOM    311  O  ASER A  22     -11.531  -3.326 -15.003  0.53  5.44           O  
+ANISOU  311  O  ASER A  22      602    786    679     59     46    138       O  
+ATOM    318  N  BPRO A  22     -14.305  -3.040 -15.563  0.47  5.18           N  
+ANISOU  318  N  BPRO A  22      713    566    690    -20    -45      8       N  
+ATOM    319  CA BPRO A  22     -13.801  -3.851 -14.452  0.47  5.29           C  
+ANISOU  319  CA BPRO A  22      701    599    711    -19    -20     59       C  
+ATOM    320  C  BPRO A  22     -12.344  -3.583 -14.119  0.47  4.84           C  
+ANISOU  320  C  BPRO A  22      590    585    664     23     27     64       C  
+ATOM    321  O  BPRO A  22     -11.499  -3.414 -15.007  0.47  5.37           O  
+ANISOU  321  O  BPRO A  22      603    762    675     65     45    100       O  
+ATOM    332  N   GLU A  23     -12.046  -3.614 -12.827  1.00  4.76           N  
+ANISOU  332  N   GLU A  23      558    607    642     79     39     69       N  
+ATOM    333  CA  GLU A  23     -10.679  -3.437 -12.387  1.00  4.89           C  
+ANISOU  333  CA  GLU A  23      576    620    663     31     42     45       C  
+ATOM    334  C   GLU A  23      -9.718  -4.412 -13.075  1.00  4.66           C  
+ANISOU  334  C   GLU A  23      509    598    663      8     21     49       C  
+ATOM    335  O   GLU A  23      -8.593  -4.031 -13.405  1.00  5.42           O  
+ANISOU  335  O   GLU A  23      569    765    725    -40     72    -21       O  
+TER     336      GLU A  23                                                      
+ENDMDL                                                                          
+END                                                                             
diff --git a/tests/data/pdb4xoj-small.pdb b/tests/data/pdb4xoj-small.pdb
new file mode 100644
index 0000000..340f13a
--- /dev/null
+++ b/tests/data/pdb4xoj-small.pdb
@@ -0,0 +1,120 @@
+ATOM    511  N   SER A  81      -2.125   6.104  21.775  1.00  8.48           N  
+ANISOU  511  N   SER A  81     1227    964   1028    -36    224     13       N  
+ATOM    512  CA  SER A  81      -1.772   4.741  22.205  1.00  8.74           C  
+ANISOU  512  CA  SER A  81     1233   1007   1077     11    199     56       C  
+ATOM    513  C   SER A  81      -2.262   3.698  21.215  1.00  8.42           C  
+ANISOU  513  C   SER A  81     1167    989   1041    -75     90    138       C  
+ATOM    514  O   SER A  81      -3.353   3.829  20.638  1.00  9.44           O  
+ANISOU  514  O   SER A  81     1153   1058   1375    -48     41     62       O  
+ATOM    515  CB  SER A  81      -2.424   4.479  23.564  1.00 10.45           C  
+ANISOU  515  CB  SER A  81     1683   1191   1094    -49    249     19       C  
+ATOM    516  OG  SER A  81      -1.889   5.387  24.506  1.00 13.63           O  
+ANISOU  516  OG  SER A  81     2449   1531   1199    -52    258     -6       O  
+ATOM    517  N  AALA A  82      -1.494   2.619  21.079  0.50  8.56           N  
+ANISOU  517  N  AALA A  82     1205    991   1055     55     81      1       N  
+ATOM    518  N  BALA A  82      -1.502   2.619  21.093  0.50  8.57           N  
+ANISOU  518  N  BALA A  82     1221    989   1047     51     73      3       N  
+ATOM    519  CA AALA A  82      -2.054   1.440  20.442  0.50  8.66           C  
+ANISOU  519  CA AALA A  82     1292    950   1046     -2     73     22       C  
+ATOM    520  CA BALA A  82      -2.004   1.455  20.381  0.50  9.05           C  
+ANISOU  520  CA BALA A  82     1452    961   1024   -102    -44     33       C  
+ATOM    521  C  AALA A  82      -3.189   0.918  21.328  0.50  8.99           C  
+ANISOU  521  C  AALA A  82     1375    993   1045     73    344    138       C  
+ATOM    522  C  BALA A  82      -3.028   0.721  21.197  0.50  9.88           C  
+ANISOU  522  C  BALA A  82     1773    960   1018   -222   -222    -32       C  
+ATOM    523  O  AALA A  82      -3.041   0.736  22.520  0.80 10.64           O  
+ANISOU  523  O  AALA A  82     1631   1389   1020   -117    191     98       O  
+ATOM    524  O  BALA A  82      -2.558   0.035  22.148  0.20  9.90           O  
+ANISOU  524  O  BALA A  82     1963   1076    722    -39     43    189       O  
+ATOM    525  CB AALA A  82      -0.983   0.385  20.289  0.50  8.83           C  
+ANISOU  525  CB AALA A  82     1351   1028    974     41    216     30       C  
+ATOM    526  CB BALA A  82      -0.809   0.503  20.120  0.50 11.15           C  
+ANISOU  526  CB BALA A  82     1719   1117   1399    107   -281   -110       C  
+ATOM    527  N   SER A  83      -4.261   0.519  20.678  1.00  9.47           N  
+ANISOU  527  N   SER A  83     1432   1102   1061   -125    244     55       N  
+ATOM    528  CA ASER A  83      -5.308  -0.275  21.345  0.70 10.42           C  
+ANISOU  528  CA ASER A  83     1524   1180   1256     61    497    220       C  
+ATOM    529  CA BSER A  83      -5.296  -0.225  21.292  0.30  9.99           C  
+ANISOU  529  CA BSER A  83     1473   1149   1171    -81    344   -232       C  
+ATOM    530  C   SER A  83      -5.324  -1.728  20.924  1.00 10.39           C  
+ANISOU  530  C   SER A  83     1457   1076   1412     -6    466    118       C  
+ATOM    531  O   SER A  83      -5.811  -2.551  21.683  1.00 12.89           O  
+ANISOU  531  O   SER A  83     2075   1194   1628    -49    830    133       O  
+ATOM    532  CB ASER A  83      -6.691   0.285  21.121  0.70 11.38           C  
+ANISOU  532  CB ASER A  83     1538   1167   1615    116    448     25       C  
+ATOM    533  CB BSER A  83      -6.610   0.424  20.946  0.30 12.23           C  
+ANISOU  533  CB BSER A  83     1463   1397   1784   -157    274   -151       C  
+ATOM    534  OG ASER A  83      -6.965   0.397  19.729  0.70 11.09           O  
+ANISOU  534  OG ASER A  83     1338   1455   1418    106    285     72       O  
+ATOM    535  OG BSER A  83      -7.621  -0.353  21.495  0.30 20.97           O  
+ANISOU  535  OG BSER A  83     2290   2191   3486    -53   1535    585       O  
+ATOM    536  N   LYS A  84      -4.827  -2.055  19.735  1.00  9.68           N  
+ANISOU  536  N   LYS A  84     1326   1010   1339    101    429     46       N  
+ATOM    537  CA ALYS A  84      -4.644  -3.431  19.279  0.70 10.05           C  
+ANISOU  537  CA ALYS A  84     1522   1007   1287     42    336    144       C  
+ATOM    538  CA BLYS A  84      -4.643  -3.451  19.329  0.30 10.14           C  
+ANISOU  538  CA BLYS A  84     1491    993   1368    139    550     68       C  
+ATOM    539  C   LYS A  84      -3.278  -3.508  18.640  1.00  9.20           C  
+ANISOU  539  C   LYS A  84     1375   1055   1064     95    218     67       C  
+ATOM    540  O   LYS A  84      -2.951  -2.592  17.884  1.00  9.59           O  
+ANISOU  540  O   LYS A  84     1298   1105   1241    165    244    147       O  
+ATOM    541  CB ALYS A  84      -5.744  -3.907  18.283  0.70 10.32           C  
+ANISOU  541  CB ALYS A  84     1408   1097   1416    -68     49    -77       C  
+ATOM    542  CB BLYS A  84      -5.751  -3.940  18.359  0.30 11.80           C  
+ANISOU  542  CB BLYS A  84     1533   1237   1712     95    111     84       C  
+ATOM    543  CG ALYS A  84      -7.150  -3.728  18.755  0.70 12.75           C  
+ANISOU  543  CG ALYS A  84     1483   1417   1942   -138    412    254       C  
+ATOM    544  CG BLYS A  84      -7.189  -3.845  18.791  0.30 12.58           C  
+ANISOU  544  CG BLYS A  84     1623   1474   1683    204    124   -240       C  
+ATOM    545  CD ALYS A  84      -8.204  -4.287  17.849  0.70 14.48           C  
+ANISOU  545  CD ALYS A  84     1679   1886   1936   -324    273    150       C  
+ATOM    546  CD BLYS A  84      -8.139  -4.069  17.666  0.30 12.72           C  
+ANISOU  546  CD BLYS A  84     1610    888   2335   -136   -285   -181       C  
+ATOM    547  CE ALYS A  84      -9.569  -4.039  18.445  0.70 21.19           C  
+ANISOU  547  CE ALYS A  84     1246   3570   3235   -471    223    759       C  
+ATOM    548  CE BLYS A  84      -9.604  -4.051  18.097  0.30 16.57           C  
+ANISOU  548  CE BLYS A  84     2201   1973   2122   -543    402   -985       C  
+ATOM    549  NZ ALYS A  84     -10.614  -4.841  17.764  0.70 22.64           N  
+ANISOU  549  NZ ALYS A  84     2289   3604   2707  -1098    686    -21       N  
+ATOM    550  NZ BLYS A  84      -9.825  -4.761  19.395  0.30 16.91           N  
+ANISOU  550  NZ BLYS A  84     1927   1989   2508   -957    607   -278       N  
+ATOM    551  N  ASER A  85      -2.563  -4.588  18.881  0.50  9.32           N  
+ANISOU  551  N  ASER A  85     1536    976   1028    171    216     66       N  
+ATOM    552  N  BSER A  85      -2.513  -4.566  18.859  0.50  9.48           N  
+ANISOU  552  N  BSER A  85     1610    922   1068    188    342     63       N  
+ATOM    553  CA ASER A  85      -1.332  -4.882  18.202  0.50  8.74           C  
+ANISOU  553  CA ASER A  85     1455   1080    786    116     49    -76       C  
+ATOM    554  CA BSER A  85      -1.229  -4.752  18.163  0.50  9.42           C  
+ANISOU  554  CA BSER A  85     1467   1050   1060    398    267     26       C  
+ATOM    555  C  ASER A  85      -1.483  -6.317  17.695  0.50  9.92           C  
+ANISOU  555  C  ASER A  85     1752    836   1179    282    208   -106       C  
+ATOM    556  C  BSER A  85      -1.244  -6.199  17.691  0.50  8.70           C  
+ANISOU  556  C  BSER A  85     1254   1236    813    315    160    171       C  
+ATOM    557  O  ASER A  85      -1.652  -7.279  18.484  0.50 11.61           O  
+ANISOU  557  O  ASER A  85     2551    941    916    222    215     86       O  
+ATOM    558  O  BSER A  85      -1.048  -7.069  18.528  0.50 10.44           O  
+ANISOU  558  O  BSER A  85     1973   1010    981    389   -113    130       O  
+ATOM    559  CB ASER A  85      -0.160  -4.700  19.129  0.50 12.48           C  
+ANISOU  559  CB ASER A  85     1350   1725   1666    185   -278     -2       C  
+ATOM    560  CB BSER A  85      -0.049  -4.451  19.125  0.50 12.99           C  
+ANISOU  560  CB BSER A  85     2150   1600   1183    804   -217   -517       C  
+ATOM    561  OG ASER A  85      -0.049  -3.356  19.526  0.50 16.00           O  
+ANISOU  561  OG ASER A  85     1752   2069   2256    354   -901   -970       O  
+ATOM    562  OG BSER A  85      -0.099  -3.127  19.634  0.50 16.22           O  
+ANISOU  562  OG BSER A  85     2356   1937   1869    867   -163   -876       O  
+ATOM    563  N   ILE A  86      -1.504  -6.433  16.390  1.00  7.88           N  
+ANISOU  563  N   ILE A  86     1184    936    872     61    178     65       N  
+ATOM    564  CA  ILE A  86      -1.872  -7.694  15.783  1.00  7.95           C  
+ANISOU  564  CA  ILE A  86     1192    863    963    -21    192    154       C  
+ATOM    565  C   ILE A  86      -0.722  -8.196  14.932  1.00  7.58           C  
+ANISOU  565  C   ILE A  86     1181    748    949   -103    205     87       C  
+ATOM    566  O   ILE A  86      -0.535  -7.767  13.777  1.00  8.17           O  
+ANISOU  566  O   ILE A  86     1249    887    967    -55    242    135       O  
+ATOM    567  CB  ILE A  86      -3.164  -7.571  14.969  1.00  8.30           C  
+ANISOU  567  CB  ILE A  86     1190    920   1043    -32    175    224       C  
+ATOM    568  CG1 ILE A  86      -4.302  -7.000  15.799  1.00  9.14           C  
+ANISOU  568  CG1 ILE A  86     1182   1078   1211     15    159    194       C  
+ATOM    569  CG2 ILE A  86      -3.524  -8.934  14.351  1.00  8.71           C  
+ANISOU  569  CG2 ILE A  86     1228    984   1097    -91     80    176       C  
+ATOM    570  CD1 ILE A  86      -5.630  -6.861  15.071  1.00 10.85           C  
+ANISOU  570  CD1 ILE A  86     1307   1331   1482     31    162    271       C  
\ No newline at end of file
diff --git a/tests/test_pdb_selaltloc.py b/tests/test_pdb_selaltloc.py
index 085376a..f977837 100644
--- a/tests/test_pdb_selaltloc.py
+++ b/tests/test_pdb_selaltloc.py
@@ -52,208 +52,6 @@ def exec_module(self):
 
         return
 
-    def test_is_same_group_1(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we are in the SAME altloc group.
-
-        previous line: ""  # first line of the PDB file
-        current  line: " ALA    1"
-
-        The result of `is_another_altloc_group` should be False.
-        """
-        result = self.module.is_another_altloc_group(
-            ' ', '', '1', '', 'ALA', '', {}, {})
-
-        self.assertFalse(result)
-
-    def test_is_same_group_2(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we are in the SAME altloc group.
-
-        All `None` case.
-
-        The result of `is_another_altloc_group` should be False.
-        """
-        result = self.module.is_another_altloc_group(
-            ' ', None, None, None, None, None, {}, {})
-
-        self.assertFalse(result)
-
-    def test_is_same_group_3(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we are in the SAME altloc group.
-
-        Example: all parameters are the same as the previous line.
-
-        previous line: "BALA   12"
-        current  line: "BALA   12"
-
-        The result of `is_another_altloc_group` should be False.
-        """
-        result = self.module.is_another_altloc_group(
-            'B', 'B', '12', '12', 'ALA', 'ALA', {'B': None},
-            {'B': {('ALA', '12')}}
-            )
-        self.assertFalse(result)
-
-
-    def test_is_same_group_4(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we are in the SAME altloc group.
-
-        Example: Multiple residue altloc. This considers altloc spanning
-        several residues. See example dummy_altloc2.pdb.
-
-        previous line: "AGLU   25"
-        current  line: "ALEU   26"
-
-        It is important to note also the dictionary input.
-
-        The result of `is_another_altloc_group` should be False.
-        """
-        result = self.module.is_another_altloc_group(
-            'A', 'A', '26', '25', 'LEU', 'GLU', {'A': ['lines']},
-            {'A': {('GLU', '25')}}
-            )
-        self.assertFalse(result)
-
-    def test_is_same_group_5(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we are in the SAME altloc group.
-
-        Example: Multiple residue altloc. This considers altloc spanning
-        several residues. See example dummy_altloc2.pdb.
-
-        previous line: " GLU   25"
-        current  line: "AALA   25"
-
-        It is important to note also the dictionary input.
-
-        The result of `is_another_altloc_group` should be False.
-        """
-        result = self.module.is_another_altloc_group(
-            'A', ' ', '25', '25', 'ALA', 'GLU', {' ': ['lines']},
-            {' ': {('GLU', '25')}}
-            )
-        self.assertFalse(result)
-
-    def test_is_another_group_1(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we entered another altloc group.
-
-        previous line: "BPRO    1"
-        current  line: " ALA    2"
-
-        The result of `is_another_altloc_group` should be True.
-        """
-        result = self.module.is_another_altloc_group(
-            ' ', 'B', '2', '1', 'ALA', 'PRO', {'B': ['lines']},
-            {'B': {('PRO', '1')}}
-            )
-        self.assertTrue(result)
-
-    def test_is_another_group_2(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we entered another altloc group.
-
-        previous line: " ALA    1"
-        current  line: " ALA    2"
-
-        The result of `is_another_altloc_group` should be True.
-        """
-        result = self.module.is_another_altloc_group(
-            ' ', ' ', '2', '1', 'ALA', 'ALA', {' ': ['lines']},
-            {' ': {('ALA', '1')}}
-            )
-        self.assertTrue(result)
-
-    def test_is_another_group_3(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we entered another altloc group.
-
-        previous line: " GLU    1"
-        current  line: " ALA    1"
-
-        The result of `is_another_altloc_group` should be True.
-        """
-        result = self.module.is_another_altloc_group(
-            ' ', ' ', '1', '1', 'ALA', 'GLU', {' ': ['lines']},
-            {' ': {('GLU', '1')}}
-            )
-        self.assertTrue(result)
-
-    def test_is_another_group_4(self):
-        """
-        Test function to identify we entered another altloc group.
-
-        This indicates we entered another altloc group.
-
-        previous line: "AGLU   25"
-        current  line: "ALEU   26"
-
-        The result of `is_another_altloc_group` should be True.
-        """
-        result = self.module.is_another_altloc_group(
-            'A', 'A', '26', '25', 'LEU', 'GLU', {' ': ['lines'], 'A': ['lines']},
-            {' ': {('LEU', '25')}, 'A': {('GLU', '26')}}
-            )
-        self.assertTrue(result)
-
-    def test_all_same_residue(self):
-        """Test all same residue."""
-        inp = {
-            ' ': [
-                    "ATOM      3  N   ASN A   1      22.066  40.557   0.420  1.00  0.00           N  ",
-                    "ATOM      3  H   ASN A   1      21.629  41.305  -0.098  1.00  0.00           H  ",
-                    "ATOM      3  H2  ASN A   1      23.236  40.798   0.369  1.00  0.00           H  ",
-                    "ATOM      3  H3  ASN A   1      21.866  40.736   1.590  1.00  0.00           H  ",
-                    ],
-            'B': ["ATOM      3  CA BASN A   1      20.000  30.000   0.005  0.60  0.00           C  "],
-            'A': ["ATOM      3  CA AASN A   1      21.411  39.311   0.054  0.40  0.00           C  "],
-            }
-
-        result = self.module.all_same_residue(inp)
-        self.assertTrue(result)
-
-    def test_all_same_residue_false(self):
-        """Test all same residue."""
-        inp = {
-            'B': ["ATOM      3  CA BSER A   2      20.000  30.000   0.005  0.60  0.00           C  "], 'A': ["ATOM      3  CA AASN A   1      21.411  39.311   0.054  0.40  0.00           C  "], } 
-        result = self.module.all_same_residue(inp)
-        self.assertFalse(result)
-
-    def test_partial_altloc(self):
-        inp = {
-            'A': [
-                    "ATOM    333  CA AGLU A  26     -10.000  -3.000 -12.000  0.50  4.89           C  ",
-                    "ANISOU  333  CA AGLU A  26      576    620    663     31     42     45       C  ",
-                 ],
-            'B':[
-                "ATOM    333  CA CGLU A  26     -10.679  -3.437 -12.387  1.00  4.89           C  ",
-                "ANISOU  333  CA CGLU A  26      576    620    663     31     42     45       C  ",
-                ],
-            }
-
-        result = self.module.partial_altloc(inp)
-        self.assertFalse(result)
-
-
     def test_default(self):
         """$ pdb_selaltloc data/dummy_altloc.pdb"""
 
@@ -266,7 +64,7 @@ def test_default(self):
 
         # Validate results
         self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 36)
+        self.assertEqual(len(self.stdout), 39)
         self.assertEqual(len(self.stderr), 0)  # no errors
 
         # Make sure sequence is correct
@@ -331,7 +129,7 @@ def test_select_loc_A(self):
 
         # Validate results
         self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 36)
+        self.assertEqual(len(self.stdout), 39)
         self.assertEqual(len(self.stderr), 0)  # no errors
 
         # Make sure sequence is correct
@@ -395,7 +193,7 @@ def test_select_loc_B(self):
 
         # Validate results
         self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 46)
+        self.assertEqual(len(self.stdout), 49)
         self.assertEqual(len(self.stderr), 0)  # no errors
 
         # Make sure sequence is correct
@@ -443,7 +241,7 @@ def test_select_loc_C(self):
 
         # Validate results
         self.assertEqual(self.retcode, 0)  # ensure the program exited OK.
-        self.assertEqual(len(self.stdout), 52)
+        self.assertEqual(len(self.stdout), 55)
         self.assertEqual(len(self.stderr), 0)  # no errors
 
         # Make sure sequence is correct
@@ -481,38 +279,56 @@ def test_select_loc_C_2(self):
 
         self.assertEqual(observed, expected)
 
-    def test_gives_same_dummy_A(self):
-        """Test dummy.pdb is not altered because there are not altlocs."""
+    def test_dummy_A(self):
+        """Test -A with dummy.pdb."""
         sys.argv = ['', '-A', os.path.join(data_dir, 'dummy.pdb')]
         self.exec_module()
         self.assertEqual(self.retcode, 0)
         self.assertEqual(len(self.stdout), 203)
         self.assertEqual(len(self.stderr), 0)
         self.assertEqual(
-            self.stdout[80],
+            self.stdout[69],
             "ATOM      3  CA  ASN A   1      21.411  39.311   0.054  0.40  0.00           C  ")
 
-    def test_gives_same_dummy_B(self):
-        """Test dummy.pdb is not altered because there are not altlocs."""
+    def test_dummy_B(self):
+        """Test -B with dummy.pdb."""
         sys.argv = ['', '-B', os.path.join(data_dir, 'dummy.pdb')]
         self.exec_module()
         self.assertEqual(self.retcode, 0)
         self.assertEqual(len(self.stdout), 203)
         self.assertEqual(len(self.stderr), 0)
         self.assertEqual(
-            self.stdout[80],
-            "ATOM      3  CA  ASN A   1      20.000  30.000   0.005  0.60  0.00           C  "
-            )
+            self.stdout[69],
+            "ATOM      3  CA  ASN A   1      20.000  30.000   0.005  0.60  0.00           C  ")
+
+    def test_gives_the_same_dummy_C(self):
+        """
+        Test -C with dummy.pdb.
+
+        Should output exactly the same PDB because there is not altloc 'C'.
+        """
+        sys.argv = ['', '-C', os.path.join(data_dir, 'dummy.pdb')]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 204)
+        self.assertEqual(len(self.stderr), 0)
+        self.assertEqual(
+            self.stdout[70],
+            "ATOM      3  CA AASN A   1      21.411  39.311   0.054  0.40  0.00           C  ")
+
+        self.assertEqual(
+            self.stdout[69],
+            "ATOM      3  CA BASN A   1      20.000  30.000   0.005  0.60  0.00           C  ")
 
     def test_gives_same_dummy_maxocc(self):
-        """Test dummy.pdb is not altered because there are not altlocs."""
+        """Test select the maximum occurance."""
         sys.argv = ['', os.path.join(data_dir, 'dummy.pdb')]
         self.exec_module()
         self.assertEqual(self.retcode, 0)
         self.assertEqual(len(self.stdout), 203)
         self.assertEqual(len(self.stderr), 0)
         self.assertEqual(
-            self.stdout[80],
+            self.stdout[69],
             "ATOM      3  CA  ASN A   1      20.000  30.000   0.005  0.60  0.00           C  "
             )
 
@@ -596,14 +412,15 @@ def test_anisou_lines(self):
         corrected.
         """
         infile = os.path.join(data_dir, 'anisou.pdb')
-        sys.argv = ['', infile]
-        self.exec_module()
-        self.assertEqual(self.retcode, 0)
-        self.assertEqual(len(self.stdout), 24)
-        self.assertEqual(len(self.stderr), 0)
-        with open(infile, "r") as fin:
-            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
-        self.assertEqual(self.stdout, expected_lines)
+        for opt in ('', '-A', '-B'):
+            sys.argv = [opt, infile]
+            self.exec_module()
+            self.assertEqual(self.retcode, 0)
+            self.assertEqual(len(self.stdout), 24)
+            self.assertEqual(len(self.stderr), 0)
+            with open(infile, "r") as fin:
+                expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+            self.assertEqual(self.stdout, expected_lines)
 
     def test_anisou_with_altloc_maxocc(self):
         """
@@ -735,11 +552,19 @@ def test_anisou_with_altloc_maxocc_B(self):
             )
 
     def test_anisou_missing(self):
-        """Test raises error if there are missing anisou lines."""
+        """
+        Works properly even when there are missing anisou lines.
+
+        In this case, it does not alter the file.
+        """
         infile = os.path.join(data_dir, 'anisou_missing.pdb')
-        sys.argv = ['', infile]
-        self.exec_module()
-        self.assertEqual(self.retcode, 0)
+        for opt in ('', '-A'):
+            sys.argv = [opt, infile]
+            self.exec_module()
+            self.assertEqual(self.retcode, 0)
+            with open(infile, "r") as fin:
+                expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+            self.assertEqual(self.stdout, expected_lines)
 
     def test_captures_previous_residue_maxocc_A(self):
         """
@@ -869,7 +694,273 @@ def test_captures_previous_residue_maxocc_B(self):
                 "ATOM    201  CB  GLY A  22      -7.405 -25.428  33.847  0.60  0.00           C  ",
                 ]
             )
+    
+    def test_handle_multiple_residues(self):
+        """
+        pdb_selaltloc data/pdb4xoj-small.pdb.
 
+        The test checks that the SER85 residue is not removed by pdb_selaltloc
+        as it happened until version 2.5.0.
+        """
+        sys.argv = ['', os.path.join(data_dir, 'pdb4xoj-small.pdb')]
+        print("executing")
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 80)
+        self.assertEqual(len(self.stderr), 0)
+        self.assertEqual(
+            self.stdout,
+            [
+                "ATOM    511  N   SER A  81      -2.125   6.104  21.775  1.00  8.48           N  ",
+                "ANISOU  511  N   SER A  81     1227    964   1028    -36    224     13       N  ",
+                "ATOM    512  CA  SER A  81      -1.772   4.741  22.205  1.00  8.74           C  ",
+                "ANISOU  512  CA  SER A  81     1233   1007   1077     11    199     56       C  ",
+                "ATOM    513  C   SER A  81      -2.262   3.698  21.215  1.00  8.42           C  ",
+                "ANISOU  513  C   SER A  81     1167    989   1041    -75     90    138       C  ",
+                "ATOM    514  O   SER A  81      -3.353   3.829  20.638  1.00  9.44           O  ",
+                "ANISOU  514  O   SER A  81     1153   1058   1375    -48     41     62       O  ",
+                "ATOM    515  CB  SER A  81      -2.424   4.479  23.564  1.00 10.45           C  ",
+                "ANISOU  515  CB  SER A  81     1683   1191   1094    -49    249     19       C  ",
+                "ATOM    516  OG  SER A  81      -1.889   5.387  24.506  1.00 13.63           O  ",
+                "ANISOU  516  OG  SER A  81     2449   1531   1199    -52    258     -6       O  ",
+                "ATOM    517  N   ALA A  82      -1.494   2.619  21.079  0.50  8.56           N  ",
+                "ANISOU  517  N   ALA A  82     1205    991   1055     55     81      1       N  ",
+                "ATOM    519  CA  ALA A  82      -2.054   1.440  20.442  0.50  8.66           C  ",
+                "ANISOU  519  CA  ALA A  82     1292    950   1046     -2     73     22       C  ",
+                "ATOM    521  C   ALA A  82      -3.189   0.918  21.328  0.50  8.99           C  ",
+                "ANISOU  521  C   ALA A  82     1375    993   1045     73    344    138       C  ",
+                "ATOM    523  O   ALA A  82      -3.041   0.736  22.520  0.80 10.64           O  ",
+                "ANISOU  523  O   ALA A  82     1631   1389   1020   -117    191     98       O  ",
+                "ATOM    525  CB  ALA A  82      -0.983   0.385  20.289  0.50  8.83           C  ",
+                "ANISOU  525  CB  ALA A  82     1351   1028    974     41    216     30       C  ",
+                "ATOM    527  N   SER A  83      -4.261   0.519  20.678  1.00  9.47           N  ",
+                "ANISOU  527  N   SER A  83     1432   1102   1061   -125    244     55       N  ",
+                "ATOM    528  CA  SER A  83      -5.308  -0.275  21.345  0.70 10.42           C  ",
+                "ANISOU  528  CA  SER A  83     1524   1180   1256     61    497    220       C  ",
+                "ATOM    530  C   SER A  83      -5.324  -1.728  20.924  1.00 10.39           C  ",
+                "ANISOU  530  C   SER A  83     1457   1076   1412     -6    466    118       C  ",
+                "ATOM    531  O   SER A  83      -5.811  -2.551  21.683  1.00 12.89           O  ",
+                "ANISOU  531  O   SER A  83     2075   1194   1628    -49    830    133       O  ",
+                "ATOM    532  CB  SER A  83      -6.691   0.285  21.121  0.70 11.38           C  ",
+                "ANISOU  532  CB  SER A  83     1538   1167   1615    116    448     25       C  ",
+                "ATOM    534  OG  SER A  83      -6.965   0.397  19.729  0.70 11.09           O  ",
+                "ANISOU  534  OG  SER A  83     1338   1455   1418    106    285     72       O  ",
+                "ATOM    536  N   LYS A  84      -4.827  -2.055  19.735  1.00  9.68           N  ",
+                "ANISOU  536  N   LYS A  84     1326   1010   1339    101    429     46       N  ",
+                "ATOM    537  CA  LYS A  84      -4.644  -3.431  19.279  0.70 10.05           C  ",
+                "ANISOU  537  CA  LYS A  84     1522   1007   1287     42    336    144       C  ",
+                "ATOM    539  C   LYS A  84      -3.278  -3.508  18.640  1.00  9.20           C  ",
+                "ANISOU  539  C   LYS A  84     1375   1055   1064     95    218     67       C  ",
+                "ATOM    540  O   LYS A  84      -2.951  -2.592  17.884  1.00  9.59           O  ",
+                "ANISOU  540  O   LYS A  84     1298   1105   1241    165    244    147       O  ",
+                "ATOM    541  CB  LYS A  84      -5.744  -3.907  18.283  0.70 10.32           C  ",
+                "ANISOU  541  CB  LYS A  84     1408   1097   1416    -68     49    -77       C  ",
+                "ATOM    543  CG  LYS A  84      -7.150  -3.728  18.755  0.70 12.75           C  ",
+                "ANISOU  543  CG  LYS A  84     1483   1417   1942   -138    412    254       C  ",
+                "ATOM    545  CD  LYS A  84      -8.204  -4.287  17.849  0.70 14.48           C  ",
+                "ANISOU  545  CD  LYS A  84     1679   1886   1936   -324    273    150       C  ",
+                "ATOM    547  CE  LYS A  84      -9.569  -4.039  18.445  0.70 21.19           C  ",
+                "ANISOU  547  CE  LYS A  84     1246   3570   3235   -471    223    759       C  ",
+                "ATOM    549  NZ  LYS A  84     -10.614  -4.841  17.764  0.70 22.64           N  ",
+                "ANISOU  549  NZ  LYS A  84     2289   3604   2707  -1098    686    -21       N  ",
+                "ATOM    551  N   SER A  85      -2.563  -4.588  18.881  0.50  9.32           N  ",
+                "ANISOU  551  N   SER A  85     1536    976   1028    171    216     66       N  ",
+                "ATOM    553  CA  SER A  85      -1.332  -4.882  18.202  0.50  8.74           C  ",
+                "ANISOU  553  CA  SER A  85     1455   1080    786    116     49    -76       C  ",
+                "ATOM    555  C   SER A  85      -1.483  -6.317  17.695  0.50  9.92           C  ",
+                "ANISOU  555  C   SER A  85     1752    836   1179    282    208   -106       C  ",
+                "ATOM    557  O   SER A  85      -1.652  -7.279  18.484  0.50 11.61           O  ",
+                "ANISOU  557  O   SER A  85     2551    941    916    222    215     86       O  ",
+                "ATOM    559  CB  SER A  85      -0.160  -4.700  19.129  0.50 12.48           C  ",
+                "ANISOU  559  CB  SER A  85     1350   1725   1666    185   -278     -2       C  ",
+                "ATOM    561  OG  SER A  85      -0.049  -3.356  19.526  0.50 16.00           O  ",
+                "ANISOU  561  OG  SER A  85     1752   2069   2256    354   -901   -970       O  ",
+                "ATOM    563  N   ILE A  86      -1.504  -6.433  16.390  1.00  7.88           N  ",
+                "ANISOU  563  N   ILE A  86     1184    936    872     61    178     65       N  ",
+                "ATOM    564  CA  ILE A  86      -1.872  -7.694  15.783  1.00  7.95           C  ",
+                "ANISOU  564  CA  ILE A  86     1192    863    963    -21    192    154       C  ",
+                "ATOM    565  C   ILE A  86      -0.722  -8.196  14.932  1.00  7.58           C  ",
+                "ANISOU  565  C   ILE A  86     1181    748    949   -103    205     87       C  ",
+                "ATOM    566  O   ILE A  86      -0.535  -7.767  13.777  1.00  8.17           O  ",
+                "ANISOU  566  O   ILE A  86     1249    887    967    -55    242    135       O  ",
+                "ATOM    567  CB  ILE A  86      -3.164  -7.571  14.969  1.00  8.30           C  ",
+                "ANISOU  567  CB  ILE A  86     1190    920   1043    -32    175    224       C  ",
+                "ATOM    568  CG1 ILE A  86      -4.302  -7.000  15.799  1.00  9.14           C  ",
+                "ANISOU  568  CG1 ILE A  86     1182   1078   1211     15    159    194       C  ",
+                "ATOM    569  CG2 ILE A  86      -3.524  -8.934  14.351  1.00  8.71           C  ",
+                "ANISOU  569  CG2 ILE A  86     1228    984   1097    -91     80    176       C  ",
+                "ATOM    570  CD1 ILE A  86      -5.630  -6.861  15.071  1.00 10.85           C  ",
+                "ANISOU  570  CD1 ILE A  86     1307   1331   1482     31    162    271       C  "
+                ]
+            )
+
+    def test_take_first(self):
+        """
+        Takes the first occurence when occ is the same and no option is given.
+
+        See: https://github.com/haddocking/pdb-tools/issues/153#issuecomment-1488627668
+        """
+        sys.argv = ['', os.path.join(data_dir, 'dummy_altloc4.pdb')]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 25)
+        self.assertEqual(len(self.stderr), 0)
+        self.assertEqual(
+            self.stdout,
+            [
+                "ATOM    153  N   VAL A  18      -0.264 -17.574  22.788  0.00  0.00           N  ",
+                "ATOM    154  CA  VAL A  18      -0.201 -17.901  24.209  0.00  0.00           C  ",
+                "ATOM    155  C   VAL A  18      -1.047 -19.150  24.437  0.00  0.00           C  ",
+                "ATOM    156  O   VAL A  18      -2.260 -19.144  24.214  0.00  0.00           O  ",
+                "ATOM    157  CB  VAL A  18      -0.689 -16.724  25.084  0.00  0.00           C  ",
+                "ATOM    161  N   TRP A  19      -0.408 -20.230  24.882  0.00  0.00           N  ",
+                "ATOM    162  CA  TRP A  19      -1.091 -21.490  25.161  0.00  0.00           C  ",
+                "ATOM    163  C   TRP A  19      -1.303 -21.563  26.667  0.00  0.00           C  ",
+                "ATOM    164  O   TRP A  19      -0.357 -21.920  27.375  0.00  0.00           O  ",
+                "ATOM    165  CB  TRP A  19      -0.272 -22.670  24.635  0.00  0.00           C  ",
+                "ATOM    176  N   TYR A  20      -2.522 -21.226  27.083  0.00  0.00           N  ",
+                "ATOM    177  CA  TYR A  20      -2.898 -21.178  28.493  0.00  0.00           C  ",
+                "ATOM    178  C   TYR A  20      -3.718 -22.410  28.851  0.00  0.00           C  ",
+                "ATOM    179  O   TYR A  20      -4.629 -22.780  28.105  0.00  0.00           O  ",
+                "ATOM    180  CB  TYR A  20      -3.681 -19.898  28.795  0.00  0.00           C  ",
+                "ATOM    189  N   VAL A  21      -3.396 -23.034  29.982  0.50  0.00           N  ",
+                "ATOM    190  CA  VAL A  21      -4.121 -24.205  30.467  0.50  0.00           C  ",
+                "ATOM    191  C   VAL A  21      -4.530 -24.072  31.930  0.50  0.00           C  ",
+                "ATOM    192  O   VAL A  21      -3.835 -23.461  32.747  0.50  0.00           O  ",
+                "ATOM    193  CB  VAL A  21      -3.289 -25.497  30.298  0.50  0.00           C  ",
+                "ATOM    189  N   PRO A  22      -3.396 -23.034  29.982  0.50  0.00           N  ",
+                "ATOM    190  CA  PRO A  22      -4.121 -24.205  30.467  0.50  0.00           C  ",
+                "ATOM    191  C   PRO A  22      -4.530 -24.072  31.930  0.50  0.00           C  ",
+                "ATOM    192  O   PRO A  22      -3.835 -23.461  32.747  0.50  0.00           O  ",
+                "ATOM    193  CB  PRO A  22      -3.289 -25.497  30.298  0.50  0.00           C  ",
+                ]
+            )
+
+    def test_mixed_occ_and_inserts(self):
+        """
+        Test mixed maximum occurence and insertion codes.
+
+        Test maximum occurence.
+        """
+        infile = os.path.join(data_dir, 'altloc_3B9F.pdb')
+        result_file = os.path.join(data_dir, 'altloc_3B9F_nooption.pdb')
+        sys.argv = ['', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
+
+    def test_mixed_occ_and_inserts_A(self):
+        """
+        Test mixed maximum occurence and insertion codes.
+
+        Test option A.
+        """
+        infile = os.path.join(data_dir, 'altloc_3B9F.pdb')
+        result_file = os.path.join(data_dir, 'altloc_3B9F_A.pdb')
+        sys.argv = ['', '-A', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
+
+    def test_mixed_occ_and_inserts_B(self):
+        """
+        Test mixed maximum occurence and insertion codes.
+
+        Test option B.
+        """
+        infile = os.path.join(data_dir, 'altloc_3B9F.pdb')
+        result_file = os.path.join(data_dir, 'altloc_3B9F_B.pdb')
+        sys.argv = ['', '-B', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
+
+    def test_with_models(self):
+        """
+        Test lines are flushed when new model found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_model.pdb')
+        sys.argv = ['', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 39)
+        self.assertEqual(len(self.stderr), 0)
+
+    def test_with_models_A(self):
+        """
+        Test lines are flushed when new model found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_model.pdb')
+        sys.argv = ['', '-A', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 39)
+        self.assertEqual(len(self.stderr), 0)
+        result = set(''.join(self.stdout).split())
+        self.assertTrue('SER' in result)
+        self.assertFalse('PRO' in result)
+
+    def test_with_models_B(self):
+        """
+        Test lines are flushed when new model found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_model.pdb')
+        sys.argv = ['', '-B', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stdout), 39)
+        result = set(''.join(self.stdout).split())
+        self.assertFalse('SER' in result)
+        self.assertTrue('PRO' in result)
+        self.assertEqual(len(self.stderr), 0)
+
+    def test_with_chains(self):
+        """
+        Test lines are flushed when new chain found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_chains.pdb')
+        result_file = os.path.join(data_dir, 'dummy_altloc_chains_maxocc.pdb')
+        sys.argv = ['', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stderr), 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
+
+    def test_with_chains_A(self):
+        """
+        Test lines are flushed when new chain found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_chains.pdb')
+        result_file = os.path.join(data_dir, 'dummy_altloc_chains_A.pdb')
+        sys.argv = ['', '-A', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stderr), 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
+
+    def test_with_chains_C(self):
+        """
+        Test lines are flushed when new chain found.
+        """
+        infile = os.path.join(data_dir, 'dummy_altloc_chains.pdb')
+        result_file = os.path.join(data_dir, 'dummy_altloc_chains_C.pdb')
+        sys.argv = ['', '-C', infile]
+        self.exec_module()
+        self.assertEqual(self.retcode, 0)
+        self.assertEqual(len(self.stderr), 0)
+        with open(result_file, "r") as fin:
+            expected_lines = [l.strip(os.linesep) for l in fin.readlines()]
+        self.assertEqual(self.stdout, expected_lines)
 
     def test_file_not_found(self):
         """$ pdb_selaltloc not_existing.pdb"""