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Merged
merged 7 commits into from
Jul 14, 2025
Merged

update PDB format #421

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1261fd4
update PDB format
yuyuan871111 Apr 12, 2025
63eee24
more clear
yuyuan871111 Apr 12, 2025
bfc3fa7
Update pdb.rst
orbeckst Jul 10, 2025
1468c43
make pre-commit happy
orbeckst Jul 10, 2025
0cf9c72
Update pdb.rst
orbeckst Jul 10, 2025
726f836
Update pdb.rst with Rocco's suggestion
orbeckst Jul 14, 2025
4c1603e
add myself in author list
yuyuan871111 Jul 14, 2025
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2 changes: 2 additions & 0 deletions doc/source/AUTHORS
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Original file line number Diff line number Diff line change
Expand Up @@ -44,3 +44,5 @@ Chronological list of authors
2024
- Mahfuza Humayra Mohona
- Rubén Chaves
2025
- Yu-Yuan (Stuart) Yang
14 changes: 13 additions & 1 deletion doc/source/formats/reference/pdb.rst
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Expand Up @@ -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
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