An abasic site is a location in DNA or RNA where a purine or pyrimidine base is missing. It is also termed an AP site (i.e., apurinic/apyrimidinic site) in biochemistry and molecular genetics. The abasic site can be formed either spontaneously (e.g., depurination) or due to DNA damage (occurring as intermediates in base excision repair). According to Wikipedia, “It has been estimated that under physiological conditions 10,000 apurinic sites and 500 apyrimidinic may be generated in a cell daily.”

In DSSR and 3DNA v2.x, nucleotides are recognized using standard atom names and base planarity. Thus, abasic sites are not taken as nucleotides (by default), simply because they do not have base atoms. DSSR introduced the --abasic option to account for abasic sites, a feature useful for detecting loops with backbone connectivity.

For example, by default, DSSR identifies one internal loop (no. 1 in the list below) in PDB entry 1l2c. With the --abasic option, two internal loops (including the one with the abasic site C.HPD18, no. 2) are detected.

List of 2 internal loops
   1 symmetric internal loop: nts=6; [1,1]; linked by [#-1,#1]
     summary: [2] 1 1 [B.1 C.24 B.3 C.22] 1 4
     nts=6 GTATAC B.DG1,B.DT2,B.DA3,C.DT22,C.DA23,C.DC24
       nts=1 T B.DT2
       nts=1 A C.DA23
   2 symmetric internal loop: nts=6; [1,1]; linked by [#1,#2]
     summary: [2] 1 1 [B.6 C.19 B.8 C.17] 4 5
     nts=6 CTTA?G B.DC6,B.DT7,B.DT8,C.DA17,C.HPD18,C.DG19
       nts=1 T B.DT7
       nts=1 ? C.HPD18

Note that C.HPD18 in 1l2c is a non-standard residue, as shown in the HETATM records below. Since the identity of C.HPD18 cannot be deduced from the atomic records, its one-letter code is designated as ?.

HETATM  346  P   HPD C  18     -14.637  52.299  29.949  1.00 49.12           P
HETATM  347  O5' HPD C  18     -14.658  52.173  28.359  1.00 48.28           O
HETATM  348  O1P HPD C  18     -15.167  51.040  30.537  1.00 49.35           O
HETATM  349  O2P HPD C  18     -13.303  52.798  30.369  1.00 46.43           O
HETATM  350  C5' HPD C  18     -15.703  51.469  27.687  1.00 45.70           C
HETATM  351  O4' HPD C  18     -16.364  50.501  25.561  1.00 44.15           O
HETATM  352  O3' HPD C  18     -13.990  51.738  24.335  1.00 45.75           O
HETATM  353  C1' HPD C  18     -16.105  54.187  25.684  1.00 52.47           C
HETATM  354  O1' HPD C  18     -17.309  54.085  26.496  1.00 56.16           O
HETATM  355  C3' HPD C  18     -14.756  52.250  25.426  1.00 46.23           C
HETATM  356  C4' HPD C  18     -15.263  51.093  26.291  1.00 45.72           C
HETATM  357  C2' HPD C  18     -16.030  52.889  24.898  1.00 49.05           C

In contrast, the R.U-8 in PDB entry 4ifd is a standard U, and is properly labeled by DSSR.

ATOM  26418  P     U R  -8     139.362  21.962 129.430  1.00208.29           P
ATOM  26419  OP1   U R  -8     140.062  20.821 130.074  1.00207.30           O
ATOM  26420  OP2   U R  -8     140.113  23.208 129.129  1.00208.44           O1+
ATOM  26421  O5'   U R  -8     138.712  21.439 128.071  1.00157.60           O
ATOM  26422  C5'   U R  -8     139.507  20.790 127.087  1.00155.47           C
ATOM  26423  C4'   U R  -8     138.843  20.804 125.731  1.00152.27           C
ATOM  26424  O4'   U R  -8     138.538  22.172 125.352  1.00149.29           O
ATOM  26425  C3'   U R  -8     139.677  20.275 124.572  1.00152.70           C
ATOM  26426  O3'   U R  -8     139.670  18.859 124.478  1.00155.04           O
ATOM  26427  C2'   U R  -8     139.053  20.969 123.369  1.00150.26           C
ATOM  26428  O2'   U R  -8     137.849  20.322 122.984  1.00146.83           O
ATOM  26429  C1'   U R  -8     138.700  22.334 123.958  1.00147.35           C

This is yet another little detail that DSSR takes care of. It is the close consideration to many such subtle points that makes DSSR different. Overall, DSSR represents my view of what a scientific software program could be (or should be).