Test of the excluded volume effects with different distance cutoffs (Dc). (A) Using a pseudoknot motif as the test system, we find that the cutoff distance of 2.8 Å can best reproduce the conformational count from exact enumeration of on-lattice conformations. (B) The triangles are the calculated entropies with cutoff distance varying from 2.2 Å to 3.4 Å. The line denotes the entropies from the on-lattice exact computer enumeration. (C) We also test the cutoff distances for different stem lengths while keeping the loop lengths fixed and (D) for different loop lengths while keeping the stem length fixed. (Dashed lines) The results with off-lattice helix and the cutoff distance; (solid lines) the results with on-lattice exact conformational enumerations. (B–D) The y-axes are the numbers of loop (L2) conformations (in log scale).
