The v2.1 release of 3DNA, currently in beta, contains many refinements of existing C programs, a complete migration from Perl scripts to Ruby, and additions of several significant new programs. All know bugs in v2.0 have been fixed. Highlights include:

• Added mutate_bases to perform in silico base mutations in nucleic-acid-containing structures (DNA, RNA, and their complexes with ligands and proteins). The program has two key and unique features: (1) the sugar-phosphate backbone conformation is untouched; (2) the base reference frame (position and orientation) is reserved, i.e., the mutated structure shares the same base-pair/step parameters as those of the native structure.
• Added x3dna_ensemble, a Ruby script to automate the processing of an NMR structure ensemble or MD trajectories in MODEL/ENDMDL delineated PDB format. It has sub-commands analyze, extract, reorient, and block_iamge. To add: convert to transform Amber, Gromacs or CHARMM trajectories.
• Enhanced find_pair with -c+ option for generating input to Curves+.
• Expanded fiber with the -s option for generating single stranded structures; the -seq option for specifying base sequence directly on the command line; and the -r option for generating RNA structures (single or double stranded) of arbitrary ACGU sequences.
• Updated the ‘baselist.dat’ file to incorporate all types of NDB/PDB nucleotides as of February 15, 2015; refined find_pair/analyze/mutate_bases etc to automatically detect and assign of modified bases.
• Renamed Atomic_a.pdb and Atomic.a.pdb etc for modified bases to account for Mac OS X filesystem case sensitivity issue; Copied all Perl scripts to a new directory perl_scripts/.
• 3DNA now generates PDB files that are compliant with PDB format v3.x, and also has option to allow for three-letter nucleotide names, thus directly compatible with PdbViewer and HADDock. An option is provided to convert 3DNA-generated base rectangular blocks in Alchemy to the more widely accepted MDL molfile format (e.g. by PyMOL).