**************************************************************************** Note: By default, each nucleotide is identified by chainId.name#. So a common case would be B.A1689, meaning adenosine #1689 on chain B. One-letter base names for modified nucleotides are put in lower case (e.g., 'c' for 5MC). For further information about the output notation, please refer to the DSSR User Manual. Questions and suggestions are *always* welcome on the 3DNA Forum. Command: x3dna-dssr -i=2bpa.pdb -o=2bpa.out File name: 2bpa.pdb no. of DNA/RNA chains: 1 [A=4] no. of nucleotides: 4 no. of atoms: 5298 no. of waters: 178 no. of metals: 0 **************************************************************************** Nucleotides not involved in stacking interactions nts=4 AAAC A.DA1,A.DA2,A.DA3,A.DC4 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=4 AAAC A.DA1,A.DA2,A.DA3,A.DC4 **************************************************************************** List of 2 splayed-apart dinucleotides 1 A.DA1 A.DA2 angle=135 distance=18.6 ratio=0.93 2 A.DA2 A.DA3 angle=121 distance=17.9 ratio=0.87 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=3 AAA A.DA1,A.DA2,A.DA3 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >2bpa nts=4 [whole] AAAC .... >2bpa-A #1 nts=4 0.70(0.41) [chain] DNA AAAC .... **************************************************************************** Summary of structural features of 4 nucleotides Note: the first five columns are: (1) serial number, (2) one-letter shorthand name, (3) dbn, (4) id string, (5) rmsd (~zero) of base ring atoms fitted against those in a standard base reference frame. The sixth (last) column contains a comma-separated list of features whose meanings are mostly self-explanatory, except for: turn: angle C1'(i-1)--C1'(i)--C1'(i+1) < 90 degrees break: no backbone linkage between O3'(i-1) and P(i) 1 A . A.DA1 0.013 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 2 A . A.DA2 0.027 turn,anti,~C3'-endo,non-stack,ss-non-loop,phosphate,splayed-apart 3 A . A.DA3 0.010 anti,~C2'-endo,non-stack,ss-non-loop,splayed-apart 4 C . A.DC4 0.010 syn,~C2'-endo,non-stack,ss-non-loop **************************************************************************** List of 5 additional files 1 dssr-2ndstrs.bpseq -- secondary structure in bpseq format 2 dssr-2ndstrs.ct -- secondary structure in connectivity table format 3 dssr-2ndstrs.dbn -- secondary structure in dot-bracket notation 4 dssr-torsions.txt -- backbone torsion angles and suite names 5 dssr-splays.pdb -- an ensemble of splayed-apart units