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I've fed these Hamiltonian cycles into Brendan McKay's NAUTY software. They fall into the following isomorphic collections:

• 6 asymmetric collections, with 48 examples of each
• 3 collections with a rotational symmetry, with 24 examples of each
• 5 collections with a reflectional symmetry, with 24 examples of each
• 2 collections with two reflectional symmetries, with 12 examples of each
• 1 collection with six-fold rotational symmetry, with 8 examples.

It makes some sense that an asymmetric cycle will have 48 examples: the specified link can be any of the 12 links, in either direction, and there is a two-fold symmetry in the graph once one directed link has been selected. This gives the correct total (using undirected counts):

6×48 + 3×24 + 5×24 + 2×12 + 1×8 = 512

See below for a picture of the last type, by the way. This uses the same vertex numbers as in the original question. From the picture, you can believe that there are two isomorphic classes of vertex, outer and inner -- different, for example, in that each outer vertex is connected to the next outer vertex in the cycle. All links are between an outer and an inner linkvertex, but there are two isomorphic classes, and the cycle alternates between them, ABABABABABAB. (You can see that they are different by comparing the result of ABA and BAB -- specifically, whether the end is connected to the start.)

I have images of the other symmetrical cycles.

Anyway, the point is that only one of the types has 3-fold symmetry -- as Robin pointed out, there must be at least one for the total to be indivisible by 3. But with only one, it will prove impossible to partition the collections into two groups of 256. This looks like bad news for a base-2 explanation of 512.

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I've fed these Hamiltonian cycles into Brendan McKay's NAUTY software. They fall into the following isomorphic collections:

• 6 asymmetric collections, with 48 examples of each
• 3 collections with a rotational symmetry, with 24 examples of each
• 5 collections with a reflectional symmetry, with 24 examples of each
• 2 collections with two reflectional symmetries, with 12 examples of each
• 1 collection with six-fold rotational symmetry, with 8 examples.

It makes some sense that an asymmetric cycle will have 48 examples: the specified link can be any of the 12 links, in either direction, and there is a two-fold symmetry in the graph once one directed link has been selected. This gives the correct total (using undirected counts):

6×48 + 3×24 + 5×24 + 2×12 + 1×8 = 512

See below for a picture of the last type, by the way. This uses the same vertex numbers as in the original question. From the picture, you can believe that there are two isomorphic classes of vertex, outer and inner -- different, for example, in that each outer vertex is connected to the next outer vertex in the cycle. All links are between an outer and an inner link, but there are two isomorphic classes, and the cycle alternates between them, ABABABABABAB. (You can see that they are different by comparing the result of ABA and BAB -- specifically, whether the end is connected to the start.)

I have images of the other symmetrical cycles.

Anyway, the point is that only one of the types has 3-fold symmetry -- as Robin pointed out, there must be at least one for the total to be indivisible by 3. But with only one, it will prove impossible to partition the collections into two groups of 256. This looks like bad news for a base-2 explanation of 512.