**************************************************************************** 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=5js1.pdb -o=5js1.out File name: 5js1.pdb no. of DNA/RNA chains: 1 [B=10] no. of nucleotides: 10 no. of atoms: 6715 no. of waters: 52 no. of metals: 1 [Mg=1] **************************************************************************** List of 3 base stacks Note: a stack is an ordered list of nucleotides assembled together via base-stacking interactions, regardless of backbone connectivity. Stacking interactions within a stem are *not* included. 1 nts=2 YU A.TYR529,B.U1 2 nts=4 RAUA A.ARG710,B.A9,B.U8,B.A7 3 nts=5 UAUCU B.U2,B.A3,B.U4,B.C5,B.U6 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=10* UUAUCUAUAA B.U1,B.U2,B.A3,B.U4,B.C5,B.U6,B.A7,B.U8,B.A9,B.A21 **************************************************************************** List of 1 splayed-apart dinucleotide 1 B.U1 B.U2 angle=148 distance=18.0 ratio=0.96 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 UU B.U1,B.U2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >5js1 nts=10 [whole] UUAUCUAUA&A .........&. >5js1-B #1 nts=10 2.43(1.37) [chain] RNA* UUAUCUAUA&A .........&. **************************************************************************** Summary of structural features of 10 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 U . B.U1 0.005 anti,non-pair-contact,ss-non-loop,phosphate,splayed-apart 2 U . B.U2 0.014 anti,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 A . B.A3 0.014 anti,BI,non-pair-contact,ss-non-loop,phosphate 4 U . B.U4 0.011 anti,BI,non-pair-contact,ss-non-loop,phosphate 5 C . B.C5 0.012 anti,BI,non-pair-contact,ss-non-loop,phosphate 6 U . B.U6 0.006 anti,BI,non-pair-contact,ss-non-loop,phosphate 7 A . B.A7 0.016 anti,BI,non-pair-contact,ss-non-loop,phosphate 8 U . B.U8 0.013 anti,non-pair-contact,ss-non-loop,phosphate 9 A . B.A9 0.007 break,anti,non-pair-contact,ss-non-loop,phosphate 10 A . B.A21 0.005 syn,~C3'-endo,ss-non-loop,phosphate **************************************************************************** List of 6 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 6 dssr-stacks.pdb -- an ensemble of base stacks