From e708aa760a4d872f6cc3691dbd6185da45909a89 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 30 Jul 2020 18:33:42 +0100
Subject: [PATCH 01/14] added HETATM fmt and conditional

---
 package/MDAnalysis/coordinates/PDB.py | 12 ++++++++++--
 1 file changed, 10 insertions(+), 2 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index fa1fac453c3..1c48fba39bc 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -528,6 +528,11 @@ class PDBWriter(base.WriterBase):
             "{chainID:1s}{resSeq:4d}{iCode:1s}"
             "   {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
             "{tempFactor:6.2f}      {segID:<4s}{element:>2s}\n"),
+        'HETATM': (
+            "HETATM{serial:5d} {name:<4s}{altLoc:<1s}{resName:<4s}"
+            "{chainID:1s}{resSeq:4d}{iCode:1s}"
+            "   {pos[0]:8.3f}{pos[1]:8.3f}{pos[2]:8.3f}{occupancy:6.2f}"
+            "{tempFactor:6.2f}      {segID:<4s}{element:>2s}\n"),
         'REMARK': "REMARK     {0}\n",
         'COMPND': "COMPND    {0}\n",
         'HEADER': "HEADER    {0}\n",
@@ -1044,8 +1049,11 @@ def get_attr(attrname, default):
             vals['segID'] = segids[i][:4]
             vals['element'] = guess_atom_element(atomnames[i].strip())[:2]
 
-            # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
-            self.pdbfile.write(self.fmt['ATOM'].format(**vals))
+            if atom.record_type == 'ATOM':
+                # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
+                self.pdbfile.write(self.fmt['ATOM'].format(**vals))
+            elif atom.record_type == 'HETATM':
+                self.pdbfile.write(self.fmt['HETATM'].format(**vals))
         if multiframe:
             self.ENDMDL()
         self.frames_written += 1

From 884d613a11cce993c8adcdde6481313f5be7ef50 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 30 Jul 2020 19:35:57 +0100
Subject: [PATCH 02/14] fix no attribute case

---
 package/MDAnalysis/coordinates/PDB.py | 17 ++++++++++++++---
 1 file changed, 14 insertions(+), 3 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 1c48fba39bc..326e979527e 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -1034,6 +1034,7 @@ def get_attr(attrname, default):
         tempfactors = get_attr('tempfactors', 0.0)
         atomnames = get_attr('names', 'X')
 
+        no_record_type = False
         for i, atom in enumerate(atoms):
             vals = {}
             vals['serial'] = util.ltruncate_int(i + 1, 5)  # check for overflow here?
@@ -1049,11 +1050,21 @@ def get_attr(attrname, default):
             vals['segID'] = segids[i][:4]
             vals['element'] = guess_atom_element(atomnames[i].strip())[:2]
 
-            if atom.record_type == 'ATOM':
+            if hasattr(atom, 'record_type'):
+                if atom.record_type == 'HETATM':
+                    # .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
+                    self.pdbfile.write(self.fmt['HETATM'].format(**vals))
+                else:
+                    # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
+                    self.pdbfile.write(self.fmt['ATOM'].format(**vals))
+            else:
                 # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
+                no_record_type = True
                 self.pdbfile.write(self.fmt['ATOM'].format(**vals))
-            elif atom.record_type == 'HETATM':
-                self.pdbfile.write(self.fmt['HETATM'].format(**vals))
+
+        if no_record_type:
+            warnings.warn("PDBWriter: No record type found for an atom - HETATM may be written out as ATOM")
+
         if multiframe:
             self.ENDMDL()
         self.frames_written += 1

From 46115cec1c1bb437d6ddd59e21ca92e83c55f1c8 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Sun, 2 Aug 2020 23:32:25 +0100
Subject: [PATCH 03/14] address reviewer's comments

---
 package/AUTHORS                               |  1 +
 package/CHANGELOG                             |  2 +
 package/MDAnalysis/coordinates/PDB.py         | 33 +++++----
 .../MDAnalysisTests/coordinates/test_pdb.py   | 71 ++++++++++++++++++-
 4 files changed, 89 insertions(+), 18 deletions(-)

diff --git a/package/AUTHORS b/package/AUTHORS
index 0d729be658a..76012d0df45 100644
--- a/package/AUTHORS
+++ b/package/AUTHORS
@@ -147,6 +147,7 @@ Chronological list of authors
   - Andrea Rizzi
   - William Glass
   - Marcello Sega
+  - Mieczyslaw Torchala
 
 External code
 -------------
diff --git a/package/CHANGELOG b/package/CHANGELOG
index 6440e9cef5a..3f729659faa 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -19,6 +19,8 @@ The rules for this file:
   * 2.0.0
 
 Fixes
+  * Instead of using ATOM for both ATOM and HETATM, HETATM record type
+    keyword is properly written out by PDB writer (Issue #1753, PR #2880)
   * Bond attribute is no longer set if PDB file contains no CONECT records
     (Issue #2832)
   * ResidueAttrs now have Atom as a target class by default; ICodes and 
diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 326e979527e..8e291267bd3 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -475,6 +475,8 @@ class PDBWriter(base.WriterBase):
     .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
     .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
     .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
+    .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
+    .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
 
 
     Note
@@ -493,6 +495,10 @@ class PDBWriter(base.WriterBase):
     are not set (:code:`None` or :code:`np.zeros(6)`,
     see Issue #2698).
 
+    When atom's record_type attribute is present (i.e. Universe object was
+    created by loading a PDB file), ATOM and HETATM record type keywords
+    are written out accordingly.
+
     See Also
     --------
     This class is identical to :class:`MultiPDBWriter` with the one
@@ -1000,6 +1006,10 @@ def _write_timestep(self, ts, multiframe=False):
            ChainID now comes from the last character of segid, as stated in the documentation.
            An indexing issue meant it previously used the first charater (Issue #2224)
 
+        .. versionchanged:: 2.0.0
+           when only record_type attribute is present, instead of using ATOM for both ATOM
+           and HETATM, HETATM record type keyword is properly written out (Issue #1753)
+
         """
         atoms = self.obj.atoms
         pos = atoms.positions
@@ -1033,8 +1043,8 @@ def get_attr(attrname, default):
         occupancies = get_attr('occupancies', 1.0)
         tempfactors = get_attr('tempfactors', 0.0)
         atomnames = get_attr('names', 'X')
+        record_types = get_attr('record_types', 'ATOM')
 
-        no_record_type = False
         for i, atom in enumerate(atoms):
             vals = {}
             vals['serial'] = util.ltruncate_int(i + 1, 5)  # check for overflow here?
@@ -1050,20 +1060,13 @@ def get_attr(attrname, default):
             vals['segID'] = segids[i][:4]
             vals['element'] = guess_atom_element(atomnames[i].strip())[:2]
 
-            if hasattr(atom, 'record_type'):
-                if atom.record_type == 'HETATM':
-                    # .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
-                    self.pdbfile.write(self.fmt['HETATM'].format(**vals))
-                else:
-                    # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
-                    self.pdbfile.write(self.fmt['ATOM'].format(**vals))
-            else:
-                # .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
-                no_record_type = True
-                self.pdbfile.write(self.fmt['ATOM'].format(**vals))
-
-        if no_record_type:
-            warnings.warn("PDBWriter: No record type found for an atom - HETATM may be written out as ATOM")
+            # record_type attribute, if exists, can be ATOM or HETATM
+            try:
+                self.pdbfile.write(self.fmt[record_types[i]].format(**vals))
+            except KeyError:
+                warnings.warn("Found '{}' for record type, but allowed types "
+                              "are ATOM or HETATM".format(record_types[i]))
+                raise ValueError
 
         if multiframe:
             self.ENDMDL()
diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index c337d54dbba..96e6e0bdea5 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -20,12 +20,12 @@
 # MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
 # J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787
 #
-import pytest
-from io import StringIO
 import os
+from io import StringIO
 
 import MDAnalysis as mda
 import numpy as np
+import pytest
 from MDAnalysisTests import make_Universe
 from MDAnalysisTests.coordinates.base import _SingleFrameReader
 from MDAnalysisTests.coordinates.reference import (RefAdKSmall,
@@ -36,7 +36,8 @@
                                        INC_PDB, PDB_xlserial, ALIGN, ENT,
                                        PDB_cm, PDB_cm_gz, PDB_cm_bz2,
                                        PDB_mc, PDB_mc_gz, PDB_mc_bz2,
-                                       PDB_CRYOEM_BOX, MMTF_NOCRYST)
+                                       PDB_CRYOEM_BOX, MMTF_NOCRYST,
+                                       PDB_HOLE, mol2_molecule)
 from numpy.testing import (assert_equal,
                            assert_array_almost_equal,
                            assert_almost_equal)
@@ -188,6 +189,14 @@ def universe2(self):
     def universe3(self):
         return mda.Universe(PDB)
 
+    @pytest.fixture
+    def universe4(self):
+        return mda.Universe(PDB_HOLE, PDB_HOLE)
+
+    @pytest.fixture
+    def universe5(self):
+        return mda.Universe(mol2_molecule, mol2_molecule)
+
     @pytest.fixture(params=[
             [PDB_CRYOEM_BOX, np.zeros(6)],
             [MMTF_NOCRYST, None]
@@ -446,6 +455,62 @@ def test_stringio_outofrange(self, universe3):
             with mda.coordinates.PDB.PDBWriter(outstring) as writer:
                 writer.write(u.atoms)
 
+    def test_hetatm_written(self, universe4, tmpdir):
+        """
+        Checks that HETATM record types are written.
+        """
+
+        u = universe4
+        u_atoms = u.select_atoms("resname ETA and record_type HETATM")
+        assert_equal(len(u_atoms), 8)
+
+        outfile = str(tmpdir.join('test-hetatm.pdb'))
+        u.atoms.write(outfile)
+        written = mda.Universe(outfile, outfile)
+        written_atoms = written.select_atoms("resname ETA and "
+                                             "record_type HETATM")
+
+        assert_equal(len(u_atoms), len(written_atoms))
+
+    def test_default_atom_record_type_written(self, universe5, tmpdir):
+        """
+        Checks that ATOM record types are written when there is no
+        record_type attribute.
+        """
+
+        u = universe5
+        outfile = str(tmpdir.join('test-mol2-to-pdb.pdb'))
+
+        expected_msg = "Found no information for attr: " \
+                       "'record_types' Using default value of 'ATOM'"
+        with pytest.warns(UserWarning, match=expected_msg):
+            u.atoms.write(outfile)
+
+        written = mda.Universe(outfile, outfile)
+        assert_equal(len(u.atoms), len(written.atoms))
+
+        atms = written.select_atoms("record_type ATOM")
+        assert_equal(len(atms.atoms), len(u.atoms))
+
+        hetatms = written.select_atoms("record_type HETATM")
+        assert_equal(len(hetatms.atoms), 0)
+
+    def test_abnormal_record_type(self, universe5, tmpdir):
+        """
+        Checks whether KeyError is raised when record type is
+        neither ATOM or HETATM.
+        """
+        u = universe5
+        u.add_TopologyAttr('record_type', ['ABNORM']*len(u.atoms))
+        outfile = str(tmpdir.join('test-abnormal-record_type.pdb'))
+
+        expected_msg = "Found 'ABNORM' for record type, but allowed " \
+                       "types are ATOM or HETATM"
+
+        with pytest.raises(ValueError):
+            with pytest.warns(UserWarning, match=expected_msg):
+                u.atoms.write(outfile)
+
 
 class TestMultiPDBReader(object):
     @staticmethod

From 9e646ecea94f543476b564a237f18665794f3b65 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Wed, 5 Aug 2020 20:01:41 +0100
Subject: [PATCH 04/14] changes as suggested by the reviewer

---
 package/CHANGELOG                     |  3 ++-
 package/MDAnalysis/coordinates/PDB.py | 29 +++++++++++++++------------
 2 files changed, 18 insertions(+), 14 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index 3f729659faa..e094b9108c9 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -14,7 +14,8 @@ The rules for this file:
 
 ------------------------------------------------------------------------------
 ??/??/?? tylerjereddy, richardjgowers, IAlibay, hmacdope, orbeckst, cbouy,
-         lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney
+         lilyminium, daveminh, jbarnoud, yuxuanzhuang, VOD555, ianmkenney,
+         mieczyslaw
 
   * 2.0.0
 
diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 8e291267bd3..78caf526ceb 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -495,9 +495,10 @@ class PDBWriter(base.WriterBase):
     are not set (:code:`None` or :code:`np.zeros(6)`,
     see Issue #2698).
 
-    When atom's record_type attribute is present (i.e. Universe object was
-    created by loading a PDB file), ATOM and HETATM record type keywords
-    are written out accordingly.
+    When the record_types attribute is present (e.g. Universe object was
+    created by loading a PDB file), ATOM_ and HETATM_ record type keywords
+    are written out accordingly. Otherwise, the ATOM_ record type is the
+    default output.
 
     See Also
     --------
@@ -998,17 +999,19 @@ def _write_timestep(self, ts, multiframe=False):
 
         .. versionchanged:: 0.7.6
            The *multiframe* keyword was added, which completely determines if
-           MODEL records are written. (Previously, this was decided based on the
-           underlying trajectory and only if ``len(traj) > 1`` would MODEL records
-           have been written.)
+           MODEL records are written. (Previously, this was decided based on
+           the underlying trajectory and only if ``len(traj) > 1`` would
+           MODEL records have been written.)
 
         .. versionchanged:: 1.0.0
-           ChainID now comes from the last character of segid, as stated in the documentation.
-           An indexing issue meant it previously used the first charater (Issue #2224)
+           ChainID now comes from the last character of segid, as stated in
+           the documentation. An indexing issue meant it previously used the
+           first charater (Issue #2224)
 
         .. versionchanged:: 2.0.0
-           when only record_type attribute is present, instead of using ATOM for both ATOM
-           and HETATM, HETATM record type keyword is properly written out (Issue #1753)
+           When only record_type attribute is present, instead of using ATOM
+           for both ATOM and HETATM, HETATM record types are properly written
+           out (Issue #1753).
 
         """
         atoms = self.obj.atoms
@@ -1064,9 +1067,9 @@ def get_attr(attrname, default):
             try:
                 self.pdbfile.write(self.fmt[record_types[i]].format(**vals))
             except KeyError:
-                warnings.warn("Found '{}' for record type, but allowed types "
-                              "are ATOM or HETATM".format(record_types[i]))
-                raise ValueError
+                errmsg = (f"Found {record_types[i]} for the record type, but "
+                          f"only allowed types are ATOM or HETATM")
+                raise ValueError(errmsg) from None
 
         if multiframe:
             self.ENDMDL()

From 0705ae8bbdf3bac0fa06886392abf581cac5386a Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 6 Aug 2020 14:41:50 +0100
Subject: [PATCH 05/14] additional comments addressed

---
 package/MDAnalysis/coordinates/PDB.py         | 21 ++++----------
 .../MDAnalysisTests/coordinates/test_pdb.py   | 29 ++++++++++---------
 2 files changed, 21 insertions(+), 29 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 78caf526ceb..58ce892a319 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -477,7 +477,9 @@ class PDBWriter(base.WriterBase):
     .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
     .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
     .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
-
+    .. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#NUMMDL
+    .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
+    .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html
 
     Note
     ----
@@ -620,10 +622,6 @@ def __init__(self, filename, bonds="conect", n_atoms=None, start=0, step=1,
            multi frame PDB file in which frames are written as MODEL_ ... ENDMDL_
            records. If ``None``, then the class default is chosen.    [``None``]
 
-        .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
-        .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-        .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-
         """
         # n_atoms = None : dummy keyword argument
         # (not used, but Writer() always provides n_atoms as the second argument)
@@ -680,9 +678,6 @@ def _write_pdb_header(self):
         unitary values (cubic box with sides of 1 Å) if unit cell dimensions
         are not set.
 
-        .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
-        .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html
-
         .. versionchanged: 1.0.0
            Fix writing of PDB file without unit cell dimensions (Issue #2679).
            If cell dimensions are not found, unitary values (cubic box with
@@ -993,13 +988,9 @@ def _write_timestep(self, ts, multiframe=False):
         :class:`PDBWriter` is in single frame mode and no MODEL_
         records are written.
 
-        .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-        .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-        .. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#NUMMDL
-
         .. versionchanged:: 0.7.6
            The *multiframe* keyword was added, which completely determines if
-           MODEL records are written. (Previously, this was decided based on
+           MODEL_ records are written. (Previously, this was decided based on
            the underlying trajectory and only if ``len(traj) > 1`` would
            MODEL records have been written.)
 
@@ -1009,8 +1000,8 @@ def _write_timestep(self, ts, multiframe=False):
            first charater (Issue #2224)
 
         .. versionchanged:: 2.0.0
-           When only record_type attribute is present, instead of using ATOM
-           for both ATOM and HETATM, HETATM record types are properly written
+           When only record_type attribute is present, instead of using ATOM_
+           for both ATOM_ and HETATM_, HETATM_ record types are properly written
            out (Issue #1753).
 
         """
diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index 96e6e0bdea5..3b27589b06a 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -191,11 +191,11 @@ def universe3(self):
 
     @pytest.fixture
     def universe4(self):
-        return mda.Universe(PDB_HOLE, PDB_HOLE)
+        return mda.Universe(PDB_HOLE)
 
     @pytest.fixture
     def universe5(self):
-        return mda.Universe(mol2_molecule, mol2_molecule)
+        return mda.Universe(mol2_molecule)
 
     @pytest.fixture(params=[
             [PDB_CRYOEM_BOX, np.zeros(6)],
@@ -461,16 +461,17 @@ def test_hetatm_written(self, universe4, tmpdir):
         """
 
         u = universe4
-        u_atoms = u.select_atoms("resname ETA and record_type HETATM")
-        assert_equal(len(u_atoms), 8)
+        u_hetatms = u.select_atoms("resname ETA and record_type HETATM")
+        assert_equal(len(u_hetatms), 8)
 
         outfile = str(tmpdir.join('test-hetatm.pdb'))
         u.atoms.write(outfile)
-        written = mda.Universe(outfile, outfile)
+        written = mda.Universe(outfile)
         written_atoms = written.select_atoms("resname ETA and "
                                              "record_type HETATM")
 
-        assert_equal(len(u_atoms), len(written_atoms))
+        assert len(u_hetatms) == len(written_atoms), "mismatched HETATM number"
+        assert_almost_equal(u_hetatms.atoms.positions, written_atoms.atoms.positions)
 
     def test_default_atom_record_type_written(self, universe5, tmpdir):
         """
@@ -481,19 +482,19 @@ def test_default_atom_record_type_written(self, universe5, tmpdir):
         u = universe5
         outfile = str(tmpdir.join('test-mol2-to-pdb.pdb'))
 
-        expected_msg = "Found no information for attr: " \
-                       "'record_types' Using default value of 'ATOM'"
+        expected_msg = ("Found no information for attr: "
+                        "'record_types' Using default value of 'ATOM'")
         with pytest.warns(UserWarning, match=expected_msg):
             u.atoms.write(outfile)
 
-        written = mda.Universe(outfile, outfile)
-        assert_equal(len(u.atoms), len(written.atoms))
+        written = mda.Universe(outfile)
+        assert len(u.atoms) == len(written.atoms), "mismatched number of atoms"
 
         atms = written.select_atoms("record_type ATOM")
-        assert_equal(len(atms.atoms), len(u.atoms))
+        assert len(atms.atoms) == len(u.atoms), "mismatched ATOM number"
 
         hetatms = written.select_atoms("record_type HETATM")
-        assert_equal(len(hetatms.atoms), 0)
+        assert len(hetatms.atoms) == 0, "mismatched HETATM number"
 
     def test_abnormal_record_type(self, universe5, tmpdir):
         """
@@ -504,8 +505,8 @@ def test_abnormal_record_type(self, universe5, tmpdir):
         u.add_TopologyAttr('record_type', ['ABNORM']*len(u.atoms))
         outfile = str(tmpdir.join('test-abnormal-record_type.pdb'))
 
-        expected_msg = "Found 'ABNORM' for record type, but allowed " \
-                       "types are ATOM or HETATM"
+        expected_msg = ("Found 'ABNORM' for record type, but allowed "
+                        "types are ATOM or HETATM")
 
         with pytest.raises(ValueError):
             with pytest.warns(UserWarning, match=expected_msg):

From 09278fcef07a2b8ba6c32e0302ea072a11e54cdd Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 6 Aug 2020 15:00:55 +0100
Subject: [PATCH 06/14] use outfile fixture

---
 testsuite/MDAnalysisTests/coordinates/test_pdb.py | 11 ++++-------
 1 file changed, 4 insertions(+), 7 deletions(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index 3b27589b06a..abfc8900cb8 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -230,7 +230,6 @@ def u_no_resids(self):
     def u_no_names(self):
         return make_Universe(['resids', 'resnames'], trajectory=True)
 
-
     def test_writer(self, universe, outfile):
         "Test writing from a single frame PDB file to a PDB file." ""
         universe.atoms.write(outfile)
@@ -455,7 +454,7 @@ def test_stringio_outofrange(self, universe3):
             with mda.coordinates.PDB.PDBWriter(outstring) as writer:
                 writer.write(u.atoms)
 
-    def test_hetatm_written(self, universe4, tmpdir):
+    def test_hetatm_written(self, universe4, tmpdir, outfile):
         """
         Checks that HETATM record types are written.
         """
@@ -464,7 +463,6 @@ def test_hetatm_written(self, universe4, tmpdir):
         u_hetatms = u.select_atoms("resname ETA and record_type HETATM")
         assert_equal(len(u_hetatms), 8)
 
-        outfile = str(tmpdir.join('test-hetatm.pdb'))
         u.atoms.write(outfile)
         written = mda.Universe(outfile)
         written_atoms = written.select_atoms("resname ETA and "
@@ -473,17 +471,17 @@ def test_hetatm_written(self, universe4, tmpdir):
         assert len(u_hetatms) == len(written_atoms), "mismatched HETATM number"
         assert_almost_equal(u_hetatms.atoms.positions, written_atoms.atoms.positions)
 
-    def test_default_atom_record_type_written(self, universe5, tmpdir):
+    def test_default_atom_record_type_written(self, universe5, tmpdir, outfile):
         """
         Checks that ATOM record types are written when there is no
         record_type attribute.
         """
 
         u = universe5
-        outfile = str(tmpdir.join('test-mol2-to-pdb.pdb'))
 
         expected_msg = ("Found no information for attr: "
                         "'record_types' Using default value of 'ATOM'")
+
         with pytest.warns(UserWarning, match=expected_msg):
             u.atoms.write(outfile)
 
@@ -496,14 +494,13 @@ def test_default_atom_record_type_written(self, universe5, tmpdir):
         hetatms = written.select_atoms("record_type HETATM")
         assert len(hetatms.atoms) == 0, "mismatched HETATM number"
 
-    def test_abnormal_record_type(self, universe5, tmpdir):
+    def test_abnormal_record_type(self, universe5, tmpdir, outfile):
         """
         Checks whether KeyError is raised when record type is
         neither ATOM or HETATM.
         """
         u = universe5
         u.add_TopologyAttr('record_type', ['ABNORM']*len(u.atoms))
-        outfile = str(tmpdir.join('test-abnormal-record_type.pdb'))
 
         expected_msg = ("Found 'ABNORM' for record type, but allowed "
                         "types are ATOM or HETATM")

From 44f63c394abe6b26c336df5c3e8add4dd673fe1d Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 6 Aug 2020 15:18:06 +0100
Subject: [PATCH 07/14] links sorted out

---
 package/MDAnalysis/coordinates/PDB.py | 37 ++++++++-------------------
 1 file changed, 11 insertions(+), 26 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 58ce892a319..54fa0d44272 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -472,14 +472,18 @@ class PDBWriter(base.WriterBase):
 
     .. _`PDB 3.2 standard`:
        http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
-    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
     .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
+    .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#COMPND
+    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
+    .. _CRYST1: http://www.wwpdb.org/documentation/file-format-content/format32/sect8.html#CRYST1
+    .. _END: http://www.wwpdb.org/documentation/file-format-content/format32/sect11.html#END
+    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
+    .. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#HEADER
     .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
+    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
     .. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#NUMMDL
-    .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
-    .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html
+    .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format32/remarks.html
+    .. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#TITLE
 
     Note
     ----
@@ -1069,8 +1073,6 @@ def get_attr(attrname, default):
     def HEADER(self, trajectory):
         """Write HEADER_ record.
 
-        .. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#HEADER
-
         .. versionchanged:: 0.20.0
             Strip `trajectory.header` since it can be modified by the user and should be
             sanitized (Issue #2324)
@@ -1083,23 +1085,16 @@ def HEADER(self, trajectory):
     def TITLE(self, *title):
         """Write TITLE_ record.
 
-        .. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html
-
         """
         line = " ".join(title)  # TODO: should do continuation automatically
         self.pdbfile.write(self.fmt['TITLE'].format(line))
 
     def REMARK(self, *remarks):
-        """Write generic REMARK_ record (without number).
+        """Write generic REMARKS_ record (without number).
 
-        Each string provided in *remarks* is written as a separate REMARK_
+        Each string provided in *remarks* is written as a separate REMARKS_
         record.
 
-        See also `REMARK (update)`_.
-
-        .. _REMARK: http://www.wwpdb.org/documentation/file-format-content/format32/remarks1.html
-        .. _REMARK (update): http://www.wwpdb.org/documentation/file-format-content/format32/remarks2.html
-
         """
         for remark in remarks:
             self.pdbfile.write(self.fmt['REMARK'].format(remark))
@@ -1129,10 +1124,6 @@ def MODEL(self, modelnumber):
            standard (i.e., 4 digits). If frame numbers are larger than
            9999, they will wrap around, i.e., 9998, 9999, 0, 1, 2, ...
 
-
-        .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-
-
         .. versionchanged:: 0.19.0
            Maximum model number is enforced.
 
@@ -1147,8 +1138,6 @@ def END(self):
         method right before closing the file it is recommended to *not* call
         :meth:`~PDBWriter.END` explicitly.
 
-        .. _END: http://www.wwpdb.org/documentation/file-format-content/format32/sect11.html#END
-
         """
         if not self.has_END:
             # only write a single END record
@@ -1158,16 +1147,12 @@ def END(self):
     def ENDMDL(self):
         """Write the ENDMDL_ record.
 
-        .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-
         """
         self.pdbfile.write(self.fmt['ENDMDL'])
 
     def CONECT(self, conect):
         """Write CONECT_ record.
 
-        .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
-
         """
         conect = ["{0:5d}".format(entry + 1) for entry in conect]
         conect = "".join(conect)

From 96fbfbcd86a3bcc8042f9e76af5e0e1ca0877be3 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Thu, 6 Aug 2020 15:39:21 +0100
Subject: [PATCH 08/14] remove duplicated _CRYST1

---
 package/MDAnalysis/coordinates/PDB.py | 1 -
 1 file changed, 1 deletion(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 54fa0d44272..9d655bcdee3 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -475,7 +475,6 @@ class PDBWriter(base.WriterBase):
     .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
     .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#COMPND
     .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
-    .. _CRYST1: http://www.wwpdb.org/documentation/file-format-content/format32/sect8.html#CRYST1
     .. _END: http://www.wwpdb.org/documentation/file-format-content/format32/sect11.html#END
     .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
     .. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#HEADER

From 31e58bbea538b7aff007b0a4e3ec6ac045928cf6 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Wed, 12 Aug 2020 15:21:50 +0100
Subject: [PATCH 09/14] address reviewer comments

---
 package/MDAnalysis/coordinates/PDB.py             |  6 +++---
 testsuite/MDAnalysisTests/coordinates/test_pdb.py | 15 +++++++++------
 2 files changed, 12 insertions(+), 9 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index 9d655bcdee3..f51d2084dcc 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -1003,9 +1003,9 @@ def _write_timestep(self, ts, multiframe=False):
            first charater (Issue #2224)
 
         .. versionchanged:: 2.0.0
-           When only record_type attribute is present, instead of using ATOM_
-           for both ATOM_ and HETATM_, HETATM_ record types are properly written
-           out (Issue #1753).
+           When only record_type attribute is present, instead of
+           using ATOM_ for both ATOM_ and HETATM_, HETATM_ record
+           types are properly written out (Issue #1753).
 
         """
         atoms = self.obj.atoms
diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index abfc8900cb8..a64c87ec80c 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -468,8 +468,10 @@ def test_hetatm_written(self, universe4, tmpdir, outfile):
         written_atoms = written.select_atoms("resname ETA and "
                                              "record_type HETATM")
 
-        assert len(u_hetatms) == len(written_atoms), "mismatched HETATM number"
-        assert_almost_equal(u_hetatms.atoms.positions, written_atoms.atoms.positions)
+        assert len(u_hetatms) == len(written_atoms), \
+            "mismatched HETATM number"
+        assert_almost_equal(u_hetatms.atoms.positions,
+                            written_atoms.atoms.positions)
 
     def test_default_atom_record_type_written(self, universe5, tmpdir, outfile):
         """
@@ -486,10 +488,12 @@ def test_default_atom_record_type_written(self, universe5, tmpdir, outfile):
             u.atoms.write(outfile)
 
         written = mda.Universe(outfile)
-        assert len(u.atoms) == len(written.atoms), "mismatched number of atoms"
+        assert len(u.atoms) == len(written.atoms), \
+            "mismatched number of atoms"
 
         atms = written.select_atoms("record_type ATOM")
-        assert len(atms.atoms) == len(u.atoms), "mismatched ATOM number"
+        assert len(atms.atoms) == len(u.atoms), \
+            "mismatched ATOM number"
 
         hetatms = written.select_atoms("record_type HETATM")
         assert len(hetatms.atoms) == 0, "mismatched HETATM number"
@@ -506,8 +510,7 @@ def test_abnormal_record_type(self, universe5, tmpdir, outfile):
                         "types are ATOM or HETATM")
 
         with pytest.raises(ValueError):
-            with pytest.warns(UserWarning, match=expected_msg):
-                u.atoms.write(outfile)
+            u.atoms.write(outfile)
 
 
 class TestMultiPDBReader(object):

From 908746f17bd6ed8daae79cf3995348c3281e4a34 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Wed, 12 Aug 2020 15:30:45 +0100
Subject: [PATCH 10/14] match exception message

---
 testsuite/MDAnalysisTests/coordinates/test_pdb.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index a64c87ec80c..749ea56be83 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -506,10 +506,10 @@ def test_abnormal_record_type(self, universe5, tmpdir, outfile):
         u = universe5
         u.add_TopologyAttr('record_type', ['ABNORM']*len(u.atoms))
 
-        expected_msg = ("Found 'ABNORM' for record type, but allowed "
-                        "types are ATOM or HETATM")
+        expected_msg = ("Found ABNORM for the record type, but only "
+                        "allowed types are ATOM or HETATM")
 
-        with pytest.raises(ValueError):
+        with pytest.raises(ValueError, match=expected_msg):
             u.atoms.write(outfile)
 
 

From d80665888b15157de570b5dbe31e3da30c354bde Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Wed, 12 Aug 2020 15:32:00 +0100
Subject: [PATCH 11/14] line lenght fix

---
 testsuite/MDAnalysisTests/coordinates/test_pdb.py | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/testsuite/MDAnalysisTests/coordinates/test_pdb.py b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
index 749ea56be83..9cd3fbc5989 100644
--- a/testsuite/MDAnalysisTests/coordinates/test_pdb.py
+++ b/testsuite/MDAnalysisTests/coordinates/test_pdb.py
@@ -473,7 +473,8 @@ def test_hetatm_written(self, universe4, tmpdir, outfile):
         assert_almost_equal(u_hetatms.atoms.positions,
                             written_atoms.atoms.positions)
 
-    def test_default_atom_record_type_written(self, universe5, tmpdir, outfile):
+    def test_default_atom_record_type_written(self, universe5, tmpdir,
+                                              outfile):
         """
         Checks that ATOM record types are written when there is no
         record_type attribute.

From 88802f99ceac3675950d26bd3c72e09e72430ee9 Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Fri, 14 Aug 2020 00:13:02 +0100
Subject: [PATCH 12/14] change PDB version to 3.3

---
 package/MDAnalysis/coordinates/PDB.py | 52 +++++++++++++--------------
 1 file changed, 26 insertions(+), 26 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index f51d2084dcc..ae0ace7a73a 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -55,7 +55,7 @@
           W.write(calphas)
 
 It is important to *always close the trajectory* when done because only at this
-step is the final END_ record written, which is required by the `PDB 3.2
+step is the final END_ record written, which is required by the `PDB 3.3
 standard`_. Using the writer as a context manager ensures that this always
 happens.
 
@@ -65,7 +65,7 @@
 
 A pure-Python implementation for PDB files commonly encountered in MD
 simulations comes under the names :class:`PDBReader` and :class:`PDBWriter`. It
-only implements a subset of the `PDB 3.2 standard`_ and also allows some
+only implements a subset of the `PDB 3.3 standard`_ and also allows some
 typical enhancements such as 4-letter resids (introduced by CHARMM/NAMD).
 
 The :class:`PDBReader` can read multi-frame PDB files and represents
@@ -136,8 +136,8 @@
    :inherited-members:
 
 
-.. _`PDB 3.2 standard`:
-    http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
+.. _`PDB 3.3 standard`:
+    http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
 
 """
 from io import StringIO, BytesIO
@@ -177,11 +177,11 @@ class PDBReader(base.ReaderBase):
     Reads multi-`MODEL`_ PDB files as trajectories.
 
     .. _PDB-formatted:
-       http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
+       http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
     .. _PDB coordinate section:
-       http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html
+       http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html
     .. _MODEL:
-       http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
+       http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
 
     =============  ============  ===========  =============================================
     COLUMNS        DATA  TYPE    FIELD        DEFINITION
@@ -459,7 +459,7 @@ def close(self):
 
 
 class PDBWriter(base.WriterBase):
-    """PDB writer that implements a subset of the `PDB 3.2 standard`_ .
+    """PDB writer that implements a subset of the `PDB 3.3 standard`_ .
 
     PDB format as used by NAMD/CHARMM: 4-letter resnames and segID are allowed,
     altLoc is written.
@@ -470,19 +470,19 @@ class PDBWriter(base.WriterBase):
     PDB "movie" (multi frame mode, *multiframe* = ``True``), consisting of
     multiple models (using the MODEL_ and ENDMDL_ records).
 
-    .. _`PDB 3.2 standard`:
-       http://www.wwpdb.org/documentation/file-format-content/format32/v3.2.html
-    .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ATOM
-    .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#COMPND
-    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
-    .. _END: http://www.wwpdb.org/documentation/file-format-content/format32/sect11.html#END
-    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-    .. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#HEADER
-    .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#HETATM
-    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-    .. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#NUMMDL
-    .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format32/remarks.html
-    .. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format32/sect2.html#TITLE
+    .. _`PDB 3.3 standard`:
+       http://www.wwpdb.org/documentation/file-format-content/format33/v3.3.html
+    .. _ATOM: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ATOM
+    .. _COMPND: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#COMPND
+    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT
+    .. _END: http://www.wwpdb.org/documentation/file-format-content/format33/sect11.html#END
+    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL
+    .. _HEADER: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#HEADER
+    .. _HETATM: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#HETATM
+    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
+    .. _NUMMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#NUMMDL
+    .. _REMARKS: http://www.wwpdb.org/documentation/file-format-content/format33/remarks.html
+    .. _TITLE: http://www.wwpdb.org/documentation/file-format-content/format33/sect2.html#TITLE
 
     Note
     ----
@@ -1161,7 +1161,7 @@ def CONECT(self, conect):
 class ExtendedPDBReader(PDBReader):
     """PDBReader that reads a PDB-formatted file with five-digit residue numbers.
 
-    This reader does not conform to the `PDB 3.2 standard`_ because it allows
+    This reader does not conform to the `PDB 3.3 standard`_ because it allows
     five-digit residue numbers that may take up columns 23 to 27 (inclusive)
     instead of being confined to 23-26 (with column 27 being reserved for the
     insertion code in the PDB standard). PDB files in this format are written
@@ -1180,7 +1180,7 @@ class ExtendedPDBReader(PDBReader):
 
 
 class MultiPDBWriter(PDBWriter):
-    """PDB writer that implements a subset of the `PDB 3.2 standard`_ .
+    """PDB writer that implements a subset of the `PDB 3.3 standard`_ .
 
     PDB format as used by NAMD/CHARMM: 4-letter resnames and segID, altLoc
     is written.
@@ -1190,9 +1190,9 @@ class MultiPDBWriter(PDBWriter):
     and ENDMDL_ records).
 
 
-    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#MODEL
-    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format32/sect9.html#ENDMDL
-    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format32/sect10.html#CONECT
+    .. _MODEL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#MODEL
+    .. _ENDMDL: http://www.wwpdb.org/documentation/file-format-content/format33/sect9.html#ENDMDL
+    .. _CONECT: http://www.wwpdb.org/documentation/file-format-content/format33/sect10.html#CONECT
 
 
     See Also

From 4b44ecbca650d9d060942d4873e59852cf20e064 Mon Sep 17 00:00:00 2001
From: Irfan Alibay <IAlibay@users.noreply.github.com>
Date: Fri, 14 Aug 2020 16:30:21 +0100
Subject: [PATCH 13/14] Issue 2906

---
 package/CHANGELOG | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/package/CHANGELOG b/package/CHANGELOG
index efdbfd0b54f..ec2a2212112 100644
--- a/package/CHANGELOG
+++ b/package/CHANGELOG
@@ -21,8 +21,8 @@ The rules for this file:
 
 Fixes
   * Instead of using ATOM for both ATOM and HETATM, HETATM record type
-    keyword is properly written out by PDB writer. Change referenced
-    PDB standard version to 3.3. (Issue #1753, PR #2880).
+    keyword is properly written out by PDB writer (Issue #1753, PR #2880).
+  * Change referenced PDB standard version to 3.3 (Issue #2906).
   * Fixed reading in masses and charges from a hoomdxml file
     (Issue #2888, PR #2889)
   * Bond attribute is no longer set if PDB file contains no CONECT records

From 6890a31eb16ead4dd85fcca1fe563e57f5e0adcd Mon Sep 17 00:00:00 2001
From: Mieczyslaw Torchala <mieczyslaw.torchala@gmail.com>
Date: Fri, 14 Aug 2020 21:28:28 +0100
Subject: [PATCH 14/14] reviewer's request

---
 package/MDAnalysis/coordinates/PDB.py | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/package/MDAnalysis/coordinates/PDB.py b/package/MDAnalysis/coordinates/PDB.py
index ae0ace7a73a..8b90c1bda9e 100644
--- a/package/MDAnalysis/coordinates/PDB.py
+++ b/package/MDAnalysis/coordinates/PDB.py
@@ -500,10 +500,10 @@ class PDBWriter(base.WriterBase):
     are not set (:code:`None` or :code:`np.zeros(6)`,
     see Issue #2698).
 
-    When the record_types attribute is present (e.g. Universe object was
-    created by loading a PDB file), ATOM_ and HETATM_ record type keywords
-    are written out accordingly. Otherwise, the ATOM_ record type is the
-    default output.
+    When the :attr:`record_types` attribute is present (e.g. Universe object
+    was created by loading a PDB file), ATOM_ and HETATM_ record type
+    keywords are written out accordingly. Otherwise, the ATOM_ record type
+    is the default output.
 
     See Also
     --------
@@ -1003,7 +1003,7 @@ def _write_timestep(self, ts, multiframe=False):
            first charater (Issue #2224)
 
         .. versionchanged:: 2.0.0
-           When only record_type attribute is present, instead of
+           When only :attr:`record_types` attribute is present, instead of
            using ATOM_ for both ATOM_ and HETATM_, HETATM_ record
            types are properly written out (Issue #1753).