- Cyclic polymers (1sfi, 6dny, 1HVZ)
- B-DNA (1bna)
- Missing carbonyl oxygen (1gfl)
- Mono-saccharides with alt locs (1B5F)
- Microheterogeneity (1EJG, 3NIR)
- PNA: peptide nucleic acid (5eme, 1xj9)
- Peptide derived residues
- Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1AUL, OMC in e.g. 5D3G)
- Bases with modified ring atoms
- DZ has C1 instead of N1 (e.g. 5I4N)
- DP has N5 instead of C5 and C7 instead of N7 (e.g. 5I4N)
- Beta & Gamma peptides (e.g. 1GAC, 6PQF)
- Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
- Polymers with residues with missing trace atoms (e.g. 2QFJ)
- Modified RNA bases (1y26, 5L4O)
- Discontinuous chains, i.e. gaps in the sequence (3sn6)
- Lots of sheets (1cbs)
- DNA (2np2, 1d66)
- C-alpha only (2rcj)
- Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
- Close backbone atoms but not linked (e.g. 4HIV)
