Thanks for visiting the 3DNA website. With the support from a dedicated NIH grant, I’ve been able to set up a domain name for 3DNA (x3dna.org) to host the homepage (http://x3dna.org) and the forum (http://forum.x3dna.org). What to know more about 3DNA? Browse around, and ask questions — I greatly appreciate all user feedback.

Listed below are news items related to 3DNA’s further development.

• 2013-05-02 (3DNA v2.1) — updated baselist.dat with nucleic-acid-containing entries in the PDB (as of May 1, 2013); revised rotate_mol and frame_mol so that atom/residue names in the original PDB file are preserved.
• 2013-04-30 — DSSR beta-r10-on-20130430 released: added a brief descriptive note and a list of generated files to the main DSSR output; revised the command-line --help with more detailed usage info; improved output format, and refined code. Now DSSR is not only self-contained, but also (at least should be) self-explanatory.
• 2013-04-21 — DSSR beta-r09-on-20130421 released: added a least-squares fitted helical axis for each identified helix/stem; classified the backbone into BI/BII conformations and the sugar into C2’/C3’-endo like (see file dssr-torsions.dat); checked for non-pairing interactions (H-bonds or base stacking) with option -non-pair; refined code and revised output format.
• 2013-03-26 (3DNA v2.1) — refined structure classification method to avoid false assignments of uncommon types (e.g., B-Z junction, W-form left-handed DNA) to structures with many non-canonical base pairs.
• 2013-03-23 — new release of DSSR-beta and 3DNA v2.1 update
  • DSSR beta-r08-on-20130323 released: refined algorithm for detecting multiplets, revised the header section to output the numbers of DNA/RNA chains, nucleotides, waters, and metals. As of this release, it appears safe to say that DSSR-beta contains all the basic features and has been well tested. The program is ready serve as a handy tool for RNA structure analysis.
  • 3DNA v2.1 has been updated with baselist.dat and atomlist.dat to accommodate all DNA/RNA entries in the latest PDB, plus minor code refinements.
• 2013-03-22 — DSSR beta-r07-on-20130322 released: code refinements, minor bug fixes, and more extensive tests; added metal info in the output.
• 2013-03-19 — DSSR beta-r06-on-20130319 released: fixed the segmentation fault bug reported by MarcParisien for PDB entry 2a64; updated the DSSR help message.
• 2013-03-16 — DSSR beta-r05-on-20130316 released: detection of ribose zippers; revision of help message; code refactoring.
• 2013-03-14 — DSSR beta-r04-on-20130314 released, with the detection of kissing loops, and revised output format.
• 2013-03-09 — DSSR beta-r03-on-20130309 released. This version was tested against all RNA/DNA-containing entries in the PDB as of March 2013, with all identified bugs fixed and internal code refinements. DSSR should now be ready for real-world applications. The first 3DNA newsletter was sent via the Forum to its 800+ registered users, announcing the availability of this DSSR release.
• 2013-03-06 — DSSR beta-r02-on-20130306 released, mostly to fix bugs reported by the first DSSR user.
• 2013-03-03 — DSSR: Software for Defining the (Secondary) Structures of RNA released (v3.0beta r01-on-20130303). The program is the first member of what would become 3DNA v3.0, and it is currently under beta testing. Yet, DSSR should be robust and efficient enough for real-world applications. It contains neat features not available in other RNA structural analysis programs.
• 2013-02-22 — fixed a documentation bug in option fiber -single: now either -single or -s works (thanks to Leonardo); revised documentation of find_pair and added an example for Curves+.
• 2013-01-28 — added RA, RA5, RA3 etc AMBER-related nucleotide names to file baselist.dat; minor refinements of documentation.
• 2013-01-26 — revised the default value of helix_break from 7.5 Å to 7.8 Å so 2o8b/c/d won’t be divided into two segments.
• 2013-01-10 — recompiled the 3DNA macosx-intel binaries on Mac OS X 10.6 (Snow Leopard) to avoid backward compatibility issue.
• 2013-01-08 — revised the algorithm for identifying nucleotides, and introduced the -ntc option for setting cutoff.
• 2012-12-29 — refined calculation of base overlap areas (to quantify stacking interactions).
• 2012-12-15 — added option analyze -ring to output centers of base ring atoms (plus base normal vectors); updated x3dna_ensemble related Ruby scripts with the corresponding functionality. This -ring option is added in response to a user request and it’s not set by default for backward compatibility.
• 2012-12-10 — updated baselist.dat to include AMBER specific nucleotides (e.g., DA5, DA3 etc); made checking of atom occupancy optional to process AMBER molecular dynamics trajectories where it is assigned 0.00.
• 2012-12-09 — miscellaneous refinements:
  • revised x3dna_ensemble to parse the section “Origin (Ox, Oy, Oz) and mean normal vector (Nx, Ny, Nz) of each base-pair in the coordinate system of the given structure” from analyses of duplexes.
  • added checking for atoms with zero occupancy — they are ignored from further analysis.
  • revised command-line help message for analyze/fiber.
• 2012-11-26 — miscellaneous refinements and minor bug fixes:
  • revised classification of chi (χ) torsion angle into syn (45° to 95°) and anti (165° to 315°) conformations.
  • modified format for listing nucleotide sequential numbers so the find_pair -c+ option interfaces better with Curves+. Spaces seem to make a difference; now use %ld instead of %5ld.
  • updated command-line documentation for fiber by adding the -rna and -seq options
• 2012-10-26 — significant functionality enhancements:
  • 3DNA now checks for each base reference frame file (Atomic*.pdb) independently: first in the current working directory, (if necessary) then the default system directory X3DNA/config. This allows for greater flexibility in picking up customized base reference frames for analysis and rebuilding.
  • Added support of 3-letter nucleotide name in base reference frame file (e.g., Atomic_5CM.pdb) so mutate_bases can now be easily applied for mutating cytosine to 5-methylcytosine.
  • Added a new FAQ entry ‘How can I mutate cytosine to 5-methylcytosine’
• 2012-10-16 — MODEL/ENDMDL delineated multiple-structure ensemble becomes default with the utility program ex_str, so the -nmr option is redundant; minor refinements of source code.
• 2012-10-06 — updated file ‘baselist.dat’ to include all canonical and modified nucleotides as of the October 6, 2012 release of PDB/NDB; added output of file ‘ref_frames.dat’ with find_pair -s option; refined atom-name parsing to accommodate AMBER generated PDB files which has e.g., "OP1 " instead of the standard compliant form " OP1".
• 2012-09-07 — added thread Datasets and scripts for reproducing Figure 5 of the 3DNA NAR03 paper on the 3DNA Forum.
• 2012-08-09 — implemented the option -chain_markers for the analysis of single-stranded DNA/RNA structures per Pascal Auffinger’s request; further code refinements.
• 2012-08-06 — added the command-line option -chain_markers to specify chain continuation character following Pascal Auffinger’s suggestion; made P…P distances and helix radii from analyze output two decimals, parameters in files bp_step.par and bp_helical.par three decimals; refined alc2img -pdb option by changing ATOM to HETATM for atomic coordinate records.
• 2012-07-26 — refined mutate_bases to take comma as well as space(s) to separate fields and updated the help file; added a corresponding command line option for each misc_3dna.par setting — e.g.,
  find_pair -max_dv=2.0 355d.pdb stdout
  to set maximum vertical separation for base pairs to 2.0 Å instead of the default 2.5 Å without modifying file misc_3dna.par.
• 2012-07-19 — updated command-line help to v2.1; added option -r to frame_mol — see the example section for a use case.
• 2012-07-09 — added option -original_bp_coordinate (can be abbreviated to -ori) to find_pair so that the identified base pairs (bp) are written in their original PDB coordinates instead of being reoriented in their bp reference frames.
• 2012-06-26 — added support for Mac OS X PPC.
• 2012-06-25 — minor refinements.
• 2012-06-22 — revised x3dna_setup to handle the most common shells bash/sh and tcsh/csh more explicitly; made PDB chain identifier case sensitive by default, i.e., ‘A’ and ‘a’ are different chains.
• 2012-06-20 — further tidy-ups and refinements
  • Refined the x3dna_setup Ruby script to take care of the tcsh/csh shell properly.
  • Made the option -pdbv3 default to comply with PDB format v3.x. The Gromacs pdb2gmx program is strict with PDB v3.x OP1/OP2 and C7 (thymine) atom naming, and DNA residue names DA/DC/DG/DT.
  • Split the following two analyze -torsion generated columns for easy parsing (thanks to Pascal Auffinger): (1) sugar-base torsion angle chi(anti/syn) from e.g. -105.9(anti) to -105.9 anti; (2) backbone BI/BII classification from e.g. 113.6(BII) to 113.6 BII.
  • Added option --single (-s) to x3dna_ensemble reorient for single-stranded nucleic acid structure.
  • Added --one (-n) option to x3dna_ensemble analyze to process only a single structure.

• 2012-06-06 — extended x3dna_ensemble (for NMR ensembles or MD trajectories) to automatically process single-stranded DNA/RNA structures [option --single (-s)] and the recently added/expanded list of torsion angles [option --torsion (-t)]; further code refactoring.
• 2012-05-04 — added the -pdb option to alc2img to readily convert 3DNA-generated alchemy files to PDB format — along with the -mol option, I’m hoping the Calladine-Drew style schematic representation of rectangular base-pair blocks would be more widely used in the community of DNA/RNA structures; tidied up code and documentation.
• 2012-05-02 — refined blocview so it now runs properly even if any third-party tool — Raster3D, PyMOL, MolScript, or ImageMagick — is not available.
• 2012-04-29 — renamed the Perl scripts (within directory $X3DNA/perl_scripts/) blocview → blocview.pl, and x3dna_setup → x3dna_setup.pl to avoid confusion with the corresponding Ruby versions within $X3DNA/bin/.
• 2012-04-25 — further tidy-ups and refinements
  • Moved all Perl scripts from bin/ into perl_scripts/ — while still available, their key functionality has now been consolidated, enhanced, and superseded by the Ruby scripts blocview, x3dna_ensemble, x3dna_setup, and x3dna_utils. Moreover, the recipes (under $X3DNA/np_recipes/) reported in the 3DNA Nature Protocols (2008) paper have been updated to work with the new Ruby scripts.
  • Refined x3dna_setup to output sensible settings for the X3DNA environment variable and PATH, even when SHELL is not set or unknown to the Ruby script.
  • Enhanced analyze to generate file stacking.pdb etc. with single-stranded DNA/RNA structures.
• 2012-04-21 — added the -enum option that enumerates all bases in a format easily adaptable to mutate_bases; as a sample application, it facilitates methylation of cytosine bases in a structure.
• 2012-04-18 — fixed a minor bug with analyze -torsion for edge cases as in PNA; updated documentation for analyze to include the -torsion option, and to explicitly specify an input file name (including ‘stdin’).
• 2012-04-16 — new features and refinements
  • added the new option -torsion to analyze to readily calculate the various DNA/RNA backbone torsion angles (α, β, γ, δ, ε, ζ, and χ), pseudo-torsions (η/θ, η′/θ′ etc), and classify backbone BI/BII, base syn/anti-conformations; to extend the Zp parameter to single-stranded DNA/RNA structures. A sample run would be analyze -torsion=6tna.txt 6tna.pdb for the yeast phenylalanine transfer RNA (6tna), and the output file is 6tna.txt.
  • extended 3DNA parser for x3dna_ensemble to include helical axis vector and position, as well as helix radii.
  • added detailed nucleotide information for each base or pair to file ref_frames.dat following analyze, e.g. 6 A-T # A:...6_:[.DA]A - B:..19_:[.DT]T
  • removed checking for mean twist angle when classifying dinucleotide steps so the B-steps in B-Z junction (2acj) are categorized.
  • added support for converting Alchmey format to molfile v3000: either specified explicitly through command line, or implicitly when the number of atoms or bonds is over 999.
• 2012-03-28 — various minor corrections and refinements
• 2012-03-13 — The v2.1beta now includes a global -pdbv3 option so that fiber/rebuild can directly generate structures compliant with PDB format v3.x; added the -molfile option in alc2img to convert 3DNA-generated base rectangular blocks in Alchemy to the MDL molfile format, which is more widely accepted (e.g., in PyMOL).
• 2012-03-09 — The v2.1beta version was updated to make 3DNA-generated PDB files compatible with HADDock and PdbViewer.
  • added option -three_letter_nts to allow for nucleotide names ADE/CYT/GUA/THY/URA in fiber/rebuild-generated strcuctures.
  • added option -connect to include CONECT records in fiber-generated models
  • For ATOM records in 3DNA generated PDB structures, set occupancy to 1.00, tempFactor to 1.00 (not 0.00, which PdbViewer complains as unrealistic B-factor), and include element symbol
  • added utility cvt2pdbv3 (within x3dna_utils) to make fiber/rebuild-generated PDB files comply with PDB format v3. Specifically, re-label O1P to OP1, O2P to OP2, and C5M to C7 for thymine. For DNA structures, also change nucleotide names from the one letter code A/C/G/T to two-letter DA/DC/DG/DT.
• 2012-03-05 — the two new sites x3dna.org and forum.x3dna.org formally replace the following three 3DNA-related websites previously hosted at Rutgers University.
  • http://rutchem.rutgers.edu/~xiangjun/3DNA — the v1.5 site which has received the most outside links, to which the ~olson variant is just a symbolic link.
  • http://3dna.rutgers.edu/ — the v2.0 site
  • http://3dna.rutgers.edu:8080/forum — the forum site