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update PDB format #421

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update PDB format #421

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1261fd4
update PDB format
yuyuan871111 Apr 12, 2025
63eee24
more clear
yuyuan871111 Apr 12, 2025
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10 changes: 9 additions & 1 deletion doc/source/formats/reference/pdb.rst
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Original file line number Diff line number Diff line change
Expand Up @@ -98,7 +98,15 @@ 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*1)
73 - 76 String segID (unofficial PDB format*2)
77 - 78 LString(2) element Element symbol, right-justified.
79 - 80 LString(2) charge Charge on the atom.
============= ============ =========== =============================================

*1(version change since 2.10.0) The columns 67-72 are not used by MDAnalysis since version 2.10.0.

*2(version change since 2.10.0) 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` to allow command-line specification.

.. _Chimera:
https://www.cgl.ucsf.edu/chimera/docs/UsersGuide/tutorials/pdbintro.html#note6
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