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+* Cyclic polymers (1sfi, 6dny, 1HVZ)
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+* B-DNA (1bna)
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+* Missing carbonyl oxygen (1gfl)
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+* Mono-saccharides with alt locs (1B5F)
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+* Microheterogeneity (1EJG, 3NIR)
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+* PNA: peptide nucleic acid (5eme, 1xj9)
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+* Peptide derived residues
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+ * GFP chromophores (5Z6Y)
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+* Nucleotides that don’t have a parent base set, i.e. detect purine/pyrimidine from geometry (THX in 1AUL, OMC in e.g. 5D3G)
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+* Bases with modified ring atoms
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+ * DZ has C1 instead of N1 (e.g. 5I4N)
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+ * DP has N5 instead of C5 and C7 instead of N7 (e.g. 5I4N)
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+* Beta & Gamma peptides (e.g. 1GAC, 6PQF)
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+* Mixed (heterogeneous) all-atom/trace-only RNA model (1JGQ)
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+* Polymers with residues with missing trace atoms (e.g. 2QFJ)
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+* Modified RNA bases (1y26, 5L4O)
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+* Discontinuous chains, i.e. gaps in the sequence (3sn6)
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+* Lots of sheets (1cbs)
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+* DNA (2np2, 1d66)
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+* C-alpha only (2rcj)
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+* Not cyclic, but termini are backbone-only and within distance but seqIds are not compatible (6SW3)
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+* Close backbone atoms but not linked (e.g. 4HIV)
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Alexander Rose