Highlights of recent developments of 3DNA/DSSR

Dear 3DNA Forum subscribers,

Here are some highlights of recent developments of 3DNA/DSSR:

Note: If you’ve difficulty in accessing the 3DNA homepage, possibly the case from mainland China (as I know it), please visit its duplicate at http://home.x3dna.org. This newsletter is written in Markdown, with a translated HTML version posted on the 3DNA homepage.

3DNA v2.3

  • The C source code is now available. Since the programs are written in strict ANSI C, 3DNA can be compiled (as is) on any computers/operating systems with a C (or C++) compiler. For user convenience, three binary distributions (with source code under the src/ subdirectory) are provided for Windows, Linux, and Mac OS X. The distributed Windows version works in native Windows (7 and up, via the cmd command-line interface, or ConEMU), MinGW/Msys (Msys2), and Cygwin, in either 32 or 64-bit.

  • A new set of ‘simple’ base-pair and step parameters was introduced to give ‘intuitive’ numerical values for non-Watson-Crick base pairs and associated steps. See the short communication titled Characterization of base pair geometry in the January 2016 issue of Computational Crystallography Newsletter (CCN).

  • The fiber program includes a new option, --pauling, for easy generation of Pauling & Corey triplex models of DNA/RNA with arbitrary base sequence. See my blogpost titled Pauling’s triplex model of nucleic acids is available in 3DNA.

  • Thomas Holder (PyMOL Principal Developer at Schrödinger, Inc.) has built a PyMOL wrapper to 3DNA fiber models. Now generating standard, regular DNA/RNA models in PyMOL is straightforward — thanks, Thomas!

DSSR (Dissecting the Spatial Structure of RNA)

  • Selected features of DSSR have been incorporated into Jmol (in collaboration with Robert Hanson, Jmol Principal Developer), and PyMOL (in collaboration with Thomas Holder). In Jmol application (via the Console window), one can now, for example, load =1ehz/dssr and then select hairpins; color red to see where the three hairpin loops are in 3D. The Jmol-DSSR web interface makes DSSR-enhanced visualization of nucleic acid structures in Jmol readily accessible to a broad user base, and has been employed in classes for educational purpose. A sample image of DSSR-derived cartoon-block representation via PyMOL is available for PDB entry 5dww, which has a G-quadruplex-duplex interface.

  • Since the publication of the Nucleic Acids Research paper in 2015, DSSR has been continuously refined and expanded, with a total of 36 new releases (from v1.2.8 to v1.6.4) as of this writing. Notably, the --json option provides DSSR-derived parameters in the simple, structured, and standard JSON format that can be easily parsed. This JSON output format is the (preferred) way for the outside world to interface with DSSR, and the Jmol-DSSR integration is built upon it. The --nmr option allows for batch processing of MODEL/ENDMDL-delineated NMR ensembles or trajectories of molecular dynamics (MD) simulations. Did you know that scripts and data files for reproducing the reported results are available in the DSSR-NAR paper section on the 3DNA Forum?

  • The User Manual is now 88-page long, covering nevertheless only the most common use cases of what DSSR has to offer. Miss a feature that you would like to have? Maybe it is already there or can be easily implemented in DSSR. Simply ask (on the 3DNA Forum), and I’ll try my best to help.

SNAP (Structures of Nucleic Acid-Protein complexes)

  • SNAP aims to consolidate, refine, and significantly extend commonly used functionalities for DNA/RNA-protein structural analysis in one easy-to-use program. Currently in beta testing, SNAP is already fully functional, with features for characterizing the protein-nucleic acid interface and identifying amino acid-base pairing and stacking interactions.

A note for 3DNA/DSSR users in mainland China: It’s a pleasure to see the ~100 registrations on the 3DNA Forum with emails ending in .cn, 163.com, or qq.com etc., mostly from recent years. I’m planning a trip to China in 2017, and I’d be happy to meet some of you for academic exchanges and possible collaborations (学术交流、合作). If you’re interested, let’s get in touch!

Best regards,

Xiang-Jun

—
Dr. Xiang-Jun Lu (律祥俊)
Email: xiangjun@x3dna.org
Web: http://home.x3dna.org/
Forum: http://forum.x3dna.org/

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Comment

Hello Xiangjun,
I want to use X3DNA-dssr but tutorial is not fruitful .I request you to send me a updated module or any tutorial stuff to use this X3DNA-DSSR i am using linux(64 bit).let me know how to integrate and use this tool means X3DNA+DSSR.

— Ram chandra Panigrahi · 2017-01-17 05:00 · #

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Hi,

Thanks for stopping by and leaving a comment.

Based on the information provided, however, I cannot figure out where the problem could be, or how I can help. Please be aware that all DSSR-related information is available from the 3DNA Forum (http://forum.x3dna.org), including a binary executable for 64-bit Linux.

Best regards,

— Xiang-Jun · 2017-01-17 08:47 · #

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Hello Xiang-Jun

I want to calculate the azimuthal orientation of DNA as mentioned in the Figure 7 of the below mentioned paper:

The structure and intermolecular forces of DNA condensates
DOI: 10.1093/nar/gkw081

My question is can we do similar kind of calculation using 3DNA?

Thanks

—Amit

— Amit · 2019-08-27 13:01 · #

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Hi Amit,

I had a quick read of Fig. 7 of the mentioned article, especially panel (A) and its caption. While the concept appears to be simple (at least in idealized cases), many details are missing for implementation of the azimuthal orientation parameter in 3DNA. Moreover, 3DNA does not currently have a similar parameter either.

It helps to ask the corresponding author for details. If provided with a concrete example, I may consider to add this azimuthal orientation parameter to 3DNA.

Best regards,

— Xiang-Jun · 2019-08-27 14:26 · #

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Thank you for printing this article from http://home.x3dna.org/. Please do not forget to visit back for more 3DNA-related information. — Xiang-Jun Lu