PDB file format

A small, highly incomplete, list of what to know about PDB formats (at least, what I found relevant but, concurrently, to so much highlighted).

WARNING: The PDB format is not updated anymore. Now the standard is the, quite heavy but coherent, mmCIF file format.

References

If specified a polymer with the characteristic Protein/Oligosaccharide (RCSB), then with have an AA bind to another molecule such as a Carbohydrate
unit cell (x-ray exp) $\neq$ biological unit. Here the guide from RCSB

Missing residues are described by the REMARK 465 record.
SEQRES describe the sequence: it contains missing residues to be compared with REMARK 465
AA that has been modified by the experimentalist, or post-translationally or other, are present with the HETATM record and described in the header with the MODRES, HET and FORMULA records
- Missing atoms that are non-standard AA are not required to be described by a MODRES record. Nevertheless, they appear in the SEQRES record
REMARK 610 describe non-polymer residues with missing atoms

Biopython
- API doc and general description
- very nicely implemented library but the documentation is far from being complete
- PDB used to read PDBs, specially ATOM records
- SeqIO used to read pdb headers and sequences. Used especially for the second case, hence bio-informatics applications.
MDAnalysis
- Used with MD trajectories for IO and analysis. Complete library with steep learning curve
openmm/pdbfixer
Modeller
- VEry complete software for a large range of application, maybe too much, and API doc which is not well structured