**************************************************************************** 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=1wwe.pdb -o=1wwe.out File name: 1wwe.pdb no. of DNA/RNA chains: 1 [B=7] no. of nucleotides: 7 no. of atoms: 1104 no. of waters: 0 no. of metals: 1 [Zn=1] **************************************************************************** List of 2 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 WG A.TRP35,B.G521 2 nts=2 UU B.U517,B.U518 **************************************************************************** Nucleotides not involved in stacking interactions nts=3 UUU B.U519,B.U520,B.U523 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=7 UUUUGCU B.U517,B.U518,B.U519,B.U520,B.G521,B.C522,B.U523 **************************************************************************** List of 3 splayed-apart dinucleotides 1 B.U518 B.U519 angle=99 distance=14.8 ratio=0.76 2 B.U519 B.U520 angle=108 distance=15.4 ratio=0.81 3 B.G521 B.C522 angle=91 distance=13.8 ratio=0.71 ---------------------------------------------------------------- Summary of 2 splayed-apart units 1 nts=3 UUU B.U518,B.U519,B.U520 2 nts=2 GC B.G521,B.C522 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >1wwe nts=7 [whole] UUUUGCU ....... >1wwe-B #1 nts=7 0.96(2.15) [chain] RNA UUUUGCU ....... **************************************************************************** Summary of structural features of 7 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.U517 0.019 anti,~C3'-endo,non-pair-contact,ss-non-loop 2 U . B.U518 0.019 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 3 U . B.U519 0.019 turn,anti,~C3'-endo,non-stack,non-pair-contact,ss-non-loop,splayed-apart 4 U . B.U520 0.019 turn,anti,non-stack,ss-non-loop,splayed-apart 5 G . B.G521 0.036 anti,~C3'-endo,non-pair-contact,ss-non-loop,splayed-apart 6 C . B.C522 0.011 anti,~C3'-endo,ss-non-loop,splayed-apart 7 U . B.U523 0.019 anti,~C3'-endo,non-stack,ss-non-loop **************************************************************************** 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