Recently, PDB begins to release atomic coordinates of large (ribosomal) structures in mmCIF format. For nucleic-acid-containing structures, the largest one so far is 4v4g, the crystal structure of five 70S ribosomes from Escherichia coli in complex with protein Y. It is assembled from ten PDB entries (1voq, 1vor, 1vos, 1vou, 1vov, 1vow, 1vox, 1voy, 1voz, 1vp0), consisting of 22,345 nucleotides, and a total of 717,805 atoms.
This humongous structure poses no problems to DSSR at all, as shown below.
Command: x3dna-dssr -i=4v4g.cif -o=4v4g.out Processing file '4v4g.cif' [4v4g] total number of base pairs: 9277 total number of multiplets: 918 total number of helices: 1099 total number of stems: 1221 total number of isolated WC/wobble pairs: 603 total number of atom-base stacking interactions: 1736 total number of hairpin loops: 504 total number of bulges: 170 total number of internal loops: 775 total number of junctions: 214 total number of non-loop single-stranded segments: 429 total number of kissing loops: 5 total number of A-minor (type I and II) motifs: 100 total number of ribose zippers: 58 (1159) total number of kink turns: 39 Time used: 00:00:10:45
It took less than 11 minutes to run on an iMac (and nearly 14 minutes on a Ubuntu Linux machine). Given the