The following cyclic nucleotides have been tested in FirstGlance version 2.8
and are believed to be handled correctly:

 - They are reported as "unusual" in an alert at the outset of a session.

 - When the red U (for Unusual) below the molecule is clicked, they are "found"
(yellow halos applied) in the "Find" dialog.

 - "Find" reports the found atoms correctly including the number of amino acid alpha carbons,
    the number of C5' atoms in nucleosides or nucleotides, and
    the number of Ligand+ atoms.

EXAMPLES OF CYCLIC NUCLEOTIDES
$ means tested successfully in FirstGlance version 2.8.

//$   CYCLIC AMP "CMP" IN 5KJX: P CONNECTED TO O3' AND O5' (6 ATOM RING) 1 group
//$   CYCLIC GMP "PCG" IN 5C8W: PA CONNECTED TO O3' AND O5' (6 ATOM RING) 6 groups
//$   CYCLIC AMP "ACK" IN 2YPE: P CONNECTED TO O2' AND O3' (5 ATOM RING) 1 group
//$   CYCLIC AM MONOPHOSPHOROTHIOATE "SP1" IN 3CF6: 3' AND 5'. 2 GROUPS
//$   SIMILAR "RP1" IN 1NE4. 2 GROUPS.
//$   "GPX" IN 1VJ7, CYCLIC GDP (3 P'S), 2' 3'. 1 GROUP.
//$   "35G" IN 1BHN, CYCLIC GMP, 6 GROUPS + 6 GDPs.
//$   "CCC" in 6dls, cyclic 2'3' CDP, 5' phosphate, 1 group with two phosphorus atoms.
//$   "A23" in 1jbr, cyclic 2'3' ADP, 5' phosphate, 1 group with two phosphorus atoms.
//$   "23G" in 5h9f, GUANOSINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
//$   "6SZ" in 5khk, 2-Aminopurine riboside-3',5'-cyclic monophosphate
//$   "6SX" in 5khi, Purine riboside-3',5'-cyclic monophosphate

EXAMPLES OF CYCLIC NUCLEOTIDES WITH CYCLIZED DIPHOSPHATES
These are seen by FirstGlance only as
"single nucleoTides, not in a chain of standard nucleotides"
FirstGlance does not look for, nor report, cyclized diphosphates.

//$   "CXR" in 2o3q, cyclic adenosine diphosphate-ribose (two riboses), 1 group.

CYCLIC NUCLEOTIDES NOT REPORTED AS UNUSUAL
These are not recognized as nucleic (nor as RNA) by JSmol.
Atoms that define nucleic in JSmol are all 9 of: C2, C3', C4, C5, C6, N1, N3, O3', O5'
(JSmol atom names: %a)
Hence they are not reported as 
"single nucleoTides, not in a chain of standard nucleotides".

//   CGR IN 2o3t CYCLIC GUANOSINE DIPHOSPHATE-RIBOSE (2 riboses)
//     Here the atoms in the 6-membered ring of guanine all have "A" appended, e.g. C2A, N3A.
//     One ribose has standard atom names. In the other, the atom names have "R" appended.
//   6SY in 5khj Uridine-3',5'-cyclic monophosphate
//     Here the atom naming does not follow the convention of using prime (') on ribose atoms.
//     Numbering in uracil is non-standard.
//   6SW in 5khh cyclic IMP
//   75G in 5t3n cyclic-2-chloro-AMP
//   N6S in 3i59, (2S)-N6-(1-Methyl-2-phenylethyl)adenosine-3',5'-cyclic monophosphate 
//   N6R in 3i59, (2R)-N6-(1-Methyl-2-phenylethyl)adenosine-3',5'-cyclic monophosphate 

NUCLEOTIDES, NOT PART OF A CHAIN, CYCLIC?
These are correctly recognized as RNA.

//   CXR in 2o3q: Cyclic ADP-ribose
//   CV1 in 3zwy, 8-bromo cyclic ADP ribose
//   N1C in 2pgl, N1-CYCLIC INOSINE 5'-DIPHOSPHORIBOSE
//   CVR in 3u4i, Cyclic adenosine 5'-diphosphocarbocyclic ribose
//   C2E in 5exx, di-cyclic-GMP
//   CCC in 6dls, cyclic CMP 5' phosphate
//   C8R in 3u4h, 8 amino cyclic inosine diphospho ribose