.. do_x3dna documentation master file, created by
   sphinx-quickstart on Thu Aug 21 15:46:15 2014.
   You can adapt this file completely to your liking, but it should at least
   contain the root `toctree` directive.

.. |3DNA package| raw:: html

   <a href="http://x3dna.org" target="_blank">3DNA package</a>

.. |mitochondrial DNA| raw:: html

   <a href="http://pdb.org/pdb/explore/explore.do?structureId=3tmm" target="_blank">mitochondrial DNA</a>

.. |nucleosome| raw:: html

   <a href="http://pdb.org/pdb/explore/explore.do?structureId=3Ut9" target="_blank">nucleosome</a>

Introduction
============

do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations.
It consists of three main components:

    * `do_x3dna <do_x3dna_usage.html>`_ ---
      To calculate structural descriptors of DNA/RNA from MD trajectory.
      Also available as a stand-alone and independent `VMD plugin <vmd_plugin.html>`_.

    * `dnaMD <dnaMD_usage.html>`_
      --- Command line tool to extract and analyze the data obtained from do_x3dna
      for **users without programming experiences**.

    * `dnaMD Python module <api_summary.html>`_
      --- To extract and analyze the data obtained from do_x3dna for
      **users with programming experiences**.

.. warning::
   DSSR-X3DNA is incompatible with do_x3dna. Please use original 3DNA packacge. 
   This could be downloaded from by `3DNA forum <http://forum.x3dna.org/site-announcements/download-instructions/>`_.

**Last Update: Feb. 2025**

**For Questions and Discussions, please visit:** `do_x3dna forum <https://groups.google.com/forum/#!forum/do_x3dna>`_.

Release Note 2025
-----------------
* Binary executable of do_x3dna is available for direct `download here <https://rjdkmr.github.io/do_x3dna/binary/do_x3dna.tar.gz>`_.
  No need to compile the code. This binary executable is compatible with tpr file generated by any GROMACS version.
* `do_x3dna <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>`_ can be compiled and 
  used with **GROMACS-2023.x, GROMACS-2024.x, GROMACS-2025.x** versions.

Release Note 2023
-----------------
* `do_x3dna <http://do-x3dna.readthedocs.io/en/latest/do_x3dna_usage.html>`_ can be compiled and used with **GROMACS-2023.x** versions.

* Support for older GROMACS (**4.5.x**, **4.6.x**, **5.0.x**, **5.1.x**, **2016.x** and **2018.x**) is **removed**.

* For above listed GROMACS version, the code is available in `2018` git branch. Please use ``git checkout 2018`` to use this version.

Release Note 2018
-----------------

   * `Added new dnaMD tools <dnaMD_usage.html#commands-table>`_

   * Added support to calculate both `global and local Elastic properties <about_dna_elasticity.html>`_

   * Added tutorials to calculate elastic properties and deformation energy
     using `dnaMD tool <global_elasticity.html>`_ and
     `dnaMD Python module <notebooks/calculate_elasticity_tutorial.html>`_.


Release Note 2017
-----------------

  * `do_x3dna <do_x3dna_usage.html>`_ can be compiled and used with **GROMACS**
    **4.5.x**, **4.6.x**, **5.0.x**, **5.1.x**, and **2016.x** versions.

  * `do_x3dna VMD plugin <vmd_plugin.html>`_

  * More user friendly --- `dnaMD <dnaMD_usage.html>`_ tools to analyze
    `do_x3dna data <do_x3dna_usage.html#output-files-table>`_ --- No
    programming experiences needed now to analyze do_x3dna data.

  * `Speed up dnaMD analysis with HDF5 file <using_hdf5.html>`_


Features
--------

.. _base-pair-image:

Base-pair parameters
~~~~~~~~~~~~~~~~~~~~

.. image:: ./images/bp_parameters.png
   :scale: 28 %
   :align: center


.. _base-step-image:

Base-step parameters
~~~~~~~~~~~~~~~~~~~~

.. image:: ./images/bps_parameters.png
   :scale: 28 %
   :align: center


.. _helical-base-step-image:

Helical Base-step parameters
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~


.. image:: ./images/bph_parameters.png
   :scale: 28 %
   :align: center


Major and minor grooves
~~~~~~~~~~~~~~~~~~~~~~~


Radius of DNA Helix
~~~~~~~~~~~~~~~~~~~


Backbone torsional angles
~~~~~~~~~~~~~~~~~~~~~~~~~

.. image:: ./images/backbone_torsions.png
   :scale: 30 %
   :align: center

**Example**: Conformational wheel using backbone torsion angles:

.. image:: ./images/backbone_torsion_wheel.png
   :scale: 70 %
   :align: center


Helical axis and its curvature
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

**Examples:**

* Bending in the helical axis of a |mitochondrial DNA|:

.. image:: ./images/p3tmm.png
   :scale: 60 %
   :align: center

-------

* Bending in the helical axis of a DNA in the |nucleosome|:

.. image:: ./images/p3ut9.png
   :scale: 70 %
   :align: center

--------


Citations
---------

**Please cite the following publications:**

* | Xiang-Jun Lu & Wilma K. Olson (2003)
  | 3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures.
  | *Nucleic Acids Res.* 31(17), 5108-21.

* | Rajendra Kumar and Helmut Grubmüller (2015)
  | `do_x3dna: a tool to analyze structural fluctuations of dsDNA or dsRNA from molecular dynamics simulations <https://doi.org/10.1093/bioinformatics/btv190>`_
  | *Bioinformatics* (2015) 31 (15): 2583-2585.


Contents
--------

.. toctree::
   :maxdepth: 1

      do_x3dna for GROMACS <install_do_x3dna>
      How to use GROMACS do_x3dna? <do_x3dna_usage>
      do_x3dna plugin for VMD  <vmd_plugin>
      Install dnaMD <install_dnaMD>
      How to use dnaMD? <dnaMD_usage>
      Speed up dnaMD with HDF5 file <using_hdf5>
      DNA elasticity - Theory <about_dna_elasticity>
      DNA elasticity - Tutorial <global_elasticity>
      dnaMD Python module Tutorial <tutorial>
      dnaMD Python module <api_summary>
      View on GitHub <https://github.com/rjdkmr/do_x3dna>


Indices and tables
==================

* :ref:`genindex`
* :ref:`modindex`
* :ref:`search`