**************************************************************************** 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=6nuh.pdb -o=6nuh.out File name: 6nuh.pdb no. of DNA/RNA chains: 1 [C=6] no. of nucleotides: 6 no. of atoms: 3956 no. of waters: 209 no. of metals: 0 **************************************************************************** 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 TC C.DT2,C.DC3 2 nts=3 WGR A.TRP67,C.DG1,A.ARG85 3 nts=3 GGA C.DG5,C.DG6,C.DA7 **************************************************************************** List of 1 non-loop single-stranded segment 1 nts=6* GTCGGA C.DG1,C.DT2,C.DC3,C.DG5,C.DG6,C.DA7 **************************************************************************** List of 1 splayed-apart dinucleotide 1 C.DG1 C.DT2 angle=105 distance=16.2 ratio=0.79 ---------------------------------------------------------------- Summary of 1 splayed-apart unit 1 nts=2 GT C.DG1,C.DT2 **************************************************************************** Secondary structures in dot-bracket notation (dbn) as a whole and per chain >6nuh nts=6 [whole] GTC&GGA ...&... >6nuh-C #1 nts=6 3.82(1.46) [chain] DNA* GTC&GGA ...&... **************************************************************************** Summary of structural features of 6 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 G . C.DG1 0.006 anti,~C2'-endo,ss-non-loop,splayed-apart 2 T . C.DT2 0.007 anti,BI,non-pair-contact,ss-non-loop,phosphate,splayed-apart 3 C . C.DC3 0.005 break,anti,~C3'-endo,non-pair-contact,ss-non-loop,phosphate 4 G . C.DG5 0.006 anti,~C3'-endo,BI,non-pair-contact,ss-non-loop 5 G . C.DG6 0.006 anti,~C2'-endo,BI,non-pair-contact,ss-non-loop 6 A . C.DA7 0.004 anti,non-pair-contact,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