X3DNA Fiber

License: X3DNA Fiber has a CC-BY-NC-4.0 license and has restrictions around commercial use and may require explicit attribution when utilized. Please refer to the license for full terms. X3DNA is user-provisioned: it is not bundled or auto-downloaded, and must be obtained yourself after free registration at x3dna.org. Please cite Lu & Olson (2003, 2008).

Proto is not affiliated with Rutgers University and Columbia University. This toolkit is open source and builds on the implementations produced by these organizations. Product names, logos, and trademarks are the property of their respective owners.

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x3dna.org

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

Xiang-Jun Lu and Wilma K Olson

Nucleic Acids Research (2003)

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@article{lu20033dna,
  title={3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures},
  author={Lu, Xiang-Jun and Olson, Wilma K},
  journal={Nucleic Acids Research},
  volume={31},
  number={17},
  pages={5108--5121},
  year={2003},
  publisher={Oxford University Press},
  doi={10.1093/nar/gkg680}
}

@article{lu20083dna,
  title={3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures},
  author={Lu, Xiang-Jun and Olson, Wilma K},
  journal={Nature Protocols},
  volume={3},
  number={7},
  pages={1213--1227},
  year={2008},
  publisher={Nature Publishing Group},
  doi={10.1038/nprot.2008.104}
}

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evo-design/proto-tools/proto_tools/tools/structure_prediction/x3dna

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Run locally with proto-tools

pip install git+https://github.com/evo-design/proto-tools.git

Toolkit contributors

Function	Description
`run_x3dna_fiber()`	Build idealized fiber DNA/RNA duplexes from base sequences with X3DNA fiber	Docs Source

Background

The fiber program in 3DNA (Lu & Olson, 2003; Lu & Olson, 2008) constructs regular helices by repeating the canonical geometry of a chosen fiber model along a user-supplied sequence. These geometries are the idealized repeating units derived from fiber-diffraction studies, most of them based on the work of Chandrasekaran & Arnott, that define the canonical A-DNA, B-DNA, and Z-DNA conformations, together with an A-form RNA duplex. Each base or base pair is placed according to the fixed helical parameters (rise, twist, and the associated base-pair geometry) of the selected form, so the result is a uniform, sequence-threaded helix. Because every base step uses the same canonical geometry, the output is an idealized model, not a structure prediction: it does not account for sequence-dependent deformation, flexibility, non-canonical pairing, or solvent and counterion effects, and no energy is computed or minimized. The models are most useful as clean, reproducible starting structures for visualization, as templates for docking or molecular-dynamics setup, or as canonical references against which experimental or predicted structures can be compared. The 3DNA/X3DNA software was originally developed by Xiang-Jun Lu while in Wilma K. Olson’s laboratory at Rutgers University and is maintained by Lu (now at Columbia University) in collaboration with Olson. The distribution is gated behind free registration on the 3DNA Forum at x3dna.org.

Learning Resources

X3DNA-DSSR homepage (Lu & Olson) - the canonical homepage, forum, downloads, and documentation, including the registration required to obtain the software.
3DNA fiber models article (Xiang-Jun Lu) - a walkthrough of the fiber program, the catalog of canonical fiber models, and the command-line interface.

Tools

X3DNA Fiber (`x3dna-fiber`)

Builds an idealized canonical fiber structure from each input base sequence and returns one Structure per sequence (the duplex by default, or the sense strand alone), exportable to PDB or mmCIF.

API Reference

Source

Input: X3DNAFiberInput

List[string]

required

Nucleotide sequences (5’->3’) for one strand of each duplex; the complementary strand is generated automatically. Bases must be A/C/G/T/U (any case). T and U are interconverted to match the requested form (T for DNA forms, U for RNA). A single string is normalized to a one-element list.

Source

Config: X3DNAFiberConfig

enum

default:"B-DNA"

Canonical helix form to build: A-DNA, B-DNA (default), Z-DNA, or RNA (A-form RNA duplex).Available options: A-DNA, B-DNA, Z-DNA, RNA

boolean

default:"False"

Output only the single (sense) strand instead of the full duplex (fiber -single). Default False.

string

Path to a local X3DNA v2.4 install root (the directory containing bin/fiber). Overrides the X3DNA environment variable and the resolved tool cache. X3DNA is user-provisioned (CC-BY-NC-4.0); see the tool README.

integer

default:"0"

Verbosity level (0=quiet, 1=info, 2=debug, 3=raw subprocess stderr). True is coerced to 1 and False to 0.

string

default:"cpu"

Device to run the tool on.

integer

default:"3600"

Maximum execution time in seconds. None waits indefinitely.

integer

Random seed. When set, tools run reproducibly up to small GPU float noise (see BaseToolOutput.approx_equal), and the seed participates in cache keys. When None, cacheable seed-sensitive tools skip cache until seeded.

Source

Output: X3DNAFiberOutput

List[Structure]

required

Idealized duplex (or single-strand) structures, one per input sequence, index-aligned with inputs.sequences.

Show Structure

string

required

Raw structure content in PDB or CIF format.

string

Format of the content string (auto-detected if omitted).

BFactorType

What the B-factor column represents.

string

Optional source identifier (filepath or tool name).

Metrics

Associated metrics (e.g., pLDDT, pTM scores, per-chain lists, pairwise matrices). None values are stripped at construction.

Applications

Use this to generate clean canonical helices from a sequence, for example to obtain a B-DNA duplex as a starting model for docking or a molecular-dynamics build, to produce an A-form RNA duplex template, or to create a canonical reference structure to compare against an experimental or predicted model. It is a generator of idealized models rather than a method for predicting the real structure of a given sequence.

Usage Tips

form (default B-DNA) selects the canonical model to build. Choose A-DNA, B-DNA, Z-DNA, or RNA (an A-form RNA duplex). T and U are interconverted automatically to match the form (T for the DNA forms, U for RNA), so the same sequence can be built in any form without manual editing.
single_stranded (default False) returns only the sense strand. Leave it False to build the full duplex with the auto-generated complement; set it True (fiber -single) when you need a single strand, such as a single-stranded RNA helix.
X3DNA must be installed by you (it is user-provisioned). X3DNA is not auto-downloaded (it is gated behind free registration at x3dna.org and distributed under CC-BY-NC-4.0). After downloading X3DNA v2.4, place it in the managed cache so bin/fiber is found automatically with no environment variable, or point the tool at the install root via the X3DNA environment variable (or PROTO_X3DNA_WEIGHTS_DIR, or the x3dna_dir config field). See SETUP.md for copy-paste steps. Without a resolvable install, the tool cannot run.

Toolkit Notes

These apply to the X3DNA Fiber tool in this toolkit (x3dna-fiber).

Runs on CPU and is deterministic. The fiber program is a fast command-line builder with no GPU and no random sampling; the same sequence and form always yield the same coordinates. Generation is near-instant for typical sequences.
User-provisioned local install only. X3DNA is gated behind free registration at x3dna.org under CC-BY-NC-4.0 and is not bundled or downloaded automatically. After downloading X3DNA v2.4, place it in the managed cache so bin/fiber resolves automatically, or expose it through the X3DNA environment variable, PROTO_X3DNA_WEIGHTS_DIR, or the x3dna_dir config field (see SETUP.md). The tool therefore runs locally with device='cpu' and is not available on hosted (device='proto') workers.
Produces idealized canonical models, not predictions. Output is a regular fiber helix with fixed canonical geometry for the chosen form; it does not model sequence-dependent deformation, non-canonical pairing, or energetics. Use a structure-prediction or refinement method when the real conformation of a specific sequence is required.

Example notebook: See the full working example for a copy-paste-ready walkthrough.

Infrastructure Guides

The following guides cover how to run tools efficiently and at scale.

Tool Persistence

Keep a tool’s model warm across calls instead of reloading it every invocation.

Device Management

How GPUs are allocated to tools and how to target specific devices.

Parallel Execution

Fan a batch of inputs out across multiple GPUs.

Tools

Guides

Tool Catalog

Concepts

Implementing a Tool

Background

Learning Resources

Tools

X3DNA Fiber (`x3dna-fiber`)

API Reference

Applications

Usage Tips

Toolkit Notes

Infrastructure Guides

Tool Persistence

Device Management

Parallel Execution

​Background

​Learning Resources

​Tools

​X3DNA Fiber (x3dna-fiber)

​API Reference

​Applications

​Usage Tips

​Toolkit Notes

​Infrastructure Guides

Tool Persistence

Device Management

Parallel Execution

Background

Learning Resources

Tools

X3DNA Fiber (`x3dna-fiber`)

API Reference

Applications

Usage Tips

Toolkit Notes

Infrastructure Guides