update PDB format (#421)

* update parsed PDB format description
* follows changes in PDBParser in MDAnalysis/mdanalysis#5001

---------

Co-authored-by: Oliver Beckstein <[email protected]>
Co-authored-by: Rocco Meli <[email protected]>

Author: 3 people

doc/source/AUTHORS

@@ -44,3 +44,5 @@ Chronological list of authors
 2024
   - Mahfuza Humayra Mohona
   - Rubén Chaves
+2025
+  - Yu-Yuan (Stuart) Yang

doc/source/formats/reference/pdb.rst

@@ -98,7 +98,19 @@ PDB specification
     47 - 54        Real(8.3)     z            Orthogonal coordinates for Z in Angstroms.
     55 - 60        Real(6.2)     occupancy    Occupancy.
     61 - 66        Real(6.2)     tempFactor   Temperature  factor.
-    67 - 76        String        segID        (unofficial CHARMM extension ?)
+    67 - 72                                   (not used in the official PDB format)
+    73 - 76        String        segID        (unofficial PDB format)
     77 - 78        LString(2)    element      Element symbol, right-justified.
     79 - 80        LString(2)    charge       Charge  on the atom.
     =============  ============  ===========  =============================================
+
+.. versionchanged:: 2.10.0
+   The columns 67-72 are not read by MDAnalysis any more.
+
+.. note::
+   The columns 73-76 are not part of the official PDB format but are used by some programs to store/operate
+   the segment ID. For instance, Chimera_ assigns it as the attribute *pdbSegment*.
+
+
+.. _Chimera:
+    https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6