3DNA: a suite of software programs for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

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.

• 2013-06-18 — DSSR beta-r13-on-20130618 released: added segid to nucleotide id string, and refined the algorithm for finding A-minor motifs.
• 2013-06-10 — DSSR beta-r12-on-20130610 released: delineated the components of bulges, internal loops, and junctions, per user request.
• 2013-06-07 (3DNA v2.1) — fixed a bug in rotate_mol/frame_mol (thanks to a bug report by Pascal Affinger); updated baselist.dat with nucleic-acid-containing entries in the PDB (as of June 7, 2013).
• 2013-06-03 — DSSR beta-r11-on-20130603 released: refined the descriptive note with help of Dr. Wilma Olson; added the --long-idstr option to explicitly delineate fields of a residue id string for easy machine parsing; added the --pucker option to output the sugar pucker following either Altona & Sundaralingam (1972) or Westhof & Sundaralingam (1983) — see the post Two slightly different definitions of sugar pucker.
• 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

3DNA is a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid-containing structures, including their complexes with proteins and other ligands. At its core, the software uses a simple matrix-based scheme for calculating a complete set of rigid-body parameters that characterize the spatial relationship of the base pairs in DNA and RNA structures. In 3DNA, structural analysis and model rebuilding are the two sides of the same coin: the description of structure is geometrically straightforward and the computation of parameters is mathematically rigorous, allowing for exact rebuilding of a molecular structure based on the derived parameters. Other unique features of 3DNA include: (1) the automatic detection of all possible base pairs, higher-order base associations and helical fragments, which makes analyzing nucleic-acid structures straightforward; (2) a comprehensive collection of 55 fiber models of regular DNA and RNA helices in various polymorphic forms and stoichiometries; (3) generation of base rectangular block schematic presentations highly effective in revealing the key features of small- to medium-sized nucleic-acid structures; (4) in silico base mutation with the sugar-phosphate backbone untouched and the original base reference frame conserved, handy for theoretical studies of DNA-protein interactions; and (5) DSSR for a comprehensive characterization of RNA (secondary) structures from three-dimensional coordinates.

3DNA is written in strict ANSI C computer language, with connecting Ruby scripts. The software package consists of over two-dozen executable programs that can be run directly from the command line in a Unix/Linux-like environment (including Mac OS X, and MinGW/MSYS and Cygwin on Windows). The software has been designed following the Unix philosophy: “Write programs that do one thing and do it well. Write programs to work together.” Each 3DNA component program aims to solve a specific set of closely related problems practically: robust and efficient, getting its job done and then out of the way. Once the user is familiar with the package, it is straightforward to combine the various pieces and other command-line-driven (or capable) tools in a script to automate commonly repeated tasks. Moreover, w3DNA provides a convenient web-interface to commonly used functionality of 3DNA, making the tool accessible to bench scientists, novices non-Linux/Unix users and for educational purposes.

3DNA originated in the SCHNAaP and SCHNArP complementary pair of programs to compute DNA rigid-body parameters and to reconstruct structures from those parameters. Our efforts to resolve the discrepancies among nucleic-acid conformational analysis programs and the consequent definition of the standard base reference frame by the structural biology community prompted us to take advantage of various features in the earlier programs and to adopt the standard frame in 3DNA. The 3DNA software was first made available on the Internet in late 1999, v1.5 was released in late 2002, and then v2.0 in 2008 to accompany the Nature Protocols paper. 3DNA is checked against all NDB entries before each major release to ensure that it works in real world applications. Over the years, we have taken each and every 3DNA-related question from a wide spectrum of user community as an opportunity to improve the functionality of the software. We strive to respond to users as quickly and concretely as possible, often with a step-by-step recipe, until an issue is resolved. This process has helped us to refine and improve the software and has prompted us to add new functionality.

Today, 3DNA has become a prominent structural bioinformatics tool, and is widely used in the scientific community. Overall, 3DNA has received near 900 citations in articles published in ~100 peer-reviewed biology, chemistry and material sciences journals. Broadly speaking, 3DNA’s applications fall into the following three categories: (1) as a standard method for nucleic acid structural analysis; (2) integrated into various structural bioinformatics resources, including the NDB and PDB; (3) enabling new scientific discoveries — 3DNA’s rigorous and reversible engine for the analysis/rebuilding of nucleic acid structures and its efficient and robust implementation in a single software package allow for new hypotheses to be formulated and validated against a large number of structures.

3DNA was initially created by Dr. Xiang-Jun Lu during 1999 to 2002 while working as a post-doctoral research associate in Dr. Wilma Olson’s laboratory at Rutgers — the State University of New Jersey. Thereafter, Dr. Lu — in collaboration with Dr. Olson — had continued to maintain and support 3DNA in his spare time as a sideline project. As of September 2011, 3DNA has been supported by an NIH R01 grant (GM096889), titled “Continued Development and Maintenance of the 3DNA Suite of Programs.” As PI of the funded project, Dr. Lu is now dedicated to pushing 3DNA to the next level to better serve the ever-changing needs of an ever-growing user community. We are working on a new release (currently in beta test) of 3DNA v2.1, which contains refinements/bug-fixes of v2.0, and significant new features.

Over the years, 3DNA had benefited greatly from interactions with the NDB project led by Professor Helen Berman. Zukang Feng at the PDB/NDB, A. R. Srinivarsan, Andrew Colasanti, Guofei Zheng, Mauricio Esguerra and other members of the Olson laboratory, Surjit Dixit (Wesleyan University), Pascal Auffinger (IBMC/CNRS, France), Ben Eisenbraun (SBGrid Consortium, Harvard Medical School), and numerous users have helped in making 3DNA a better tool to serve the scientific community.

The 3DNA software, its homepage and forum have been created and maintained by Xiang-Jun Lu. Unless specified explicitly otherwise, all posts at x3dna.org are written by Xiang-Jun Lu. The favicon and logo of the homepage and the forum were designed by Jessalyn Lu. The three 3DNA-related services — w3DNA, 3DNALandscapes and BPS — are supported by the Olson laboratory at Rutgers University.

The 3DNA project is supported by the NIH grant R01GM096889.