Installation

The latest 3DNA v2.0, with recipes and associated data files for the Nature Protocols manuscript, is distributed in a tarball file named X3DNA.tar.gz. The tarball link given here is for the reviewing process of our 3DNA manuscript: the 3DNA C binaries have been compiled on Ubuntu Linux and should run on other flavors of Intel-based Linux distributions. To install, download it to a directory of your choice, presumably your home directory, and then do the following:

  1. tar zxvf X3DNA.tar.gz
  2. cd X3DNA/bin
  3. x3dna_setup
    It will output message like the following (for my computer settings):
            To run X3DNA, you need to set up the followings:
              o the environment variable X3DNA
              o add $X3DNA/bin to your command line search path
            for your 'bash' shell, please add the following into ~/.bashrc:
              --------------------------------------------------------------
                export X3DNA=/home/xiangjun/X3DNA
                export PATH=/home/xiangjun/X3DNA/bin:$PATH
              --------------------------------------------------------------
    
  4. type find_pair -h for command line help -- this applies to all 3DNA binaries. Visit 3DNA homepage at URL http://3dna.rutgers.edu/

Play with the Recipes

The recipes related to the Nature Protocols manuscript is under directory $X3DNA/NP_Recipes where there is a README file. Read it through and check each sub-directory for details.

In particular, there is a separate directory for each Recipe mentioned in the 3DNA manuscript that contains all the script(s), data files and the final generated image(s) directly used in the manuscript. For verification purpose, it would help to firstly make a copy of the directory NP_Recipes to a new location, e.g., NP_Recipes_play (using "cp -r") and play from there.

With the software tools mentioned in the next section properly installed, re-running the seven Recipe scripts takes less than thirty minutes on my Linux box.

Links

Here is a list of the software mentioned in the manuscript. They are readily available and are of great value to our own research. Please note that the software listed below are only used in the visualization part of 3DNA, e.g., for creating the figures used in the 3DNA manuscript. The analysis and rebuilding parts of 3DNA have zero dependence on third-part tools.

  1. RasMol There are many variants available, each with claimed new functionality. However, unless well tested, some also introduced bugs. Specifically, the v2.7.x series do not handle the Alchemy format right. I've been using v2.6.4, the version directly from Roger Sayle, the original author of RasMol. While RasMol is not directly used in generating the images used in the 3DNA manuscript, it is nevertheless a handy light-weighted tool for molecular structure visualization, especially for Alchemy files (which PyMOL seems do not like).
  2. MolScript It is used to generate Raster3D scenes of protein ribbons and nucleic acid backbone.
  3. Raster3D All 3DNA generated raster-graphics images are in Raster3D ".r3d" format. Only render is used in 3DNA.
  4. PyMOL While PyMOL is most commonly used interactively, we have explored its scripting capability (".pml" script) in 3DNA for integration with other command-line driven tools. Of course, one can easily load the ".r3d" files into PyMOL to interactively play with them, just as with the normal Raster3D/MolSctipt to PyMOL interface.
  5. Ghostscript It is used for converting an EPS file to a PNG image at a specific resolution (300 DPI for the figures in the manuscript).
  6. ImageMagick This is a very useful general-purpose image processing toolset. I have been using its display and convert on a regular basis.
  7. Xfig I like Xfig for its simplicity, quality, and availability and it fulfills my purposes nicely for line-drawing and composing composite figures. In particular, it allows for direct editing of the Xfig files generated from 3DNA. In retrospect, 3DNA's support for Xfig was added after EPS. Using the utility program pstoedit, one can easily convert 3DNA generated EPS file to Xfig format. However, the more I play with Xfig, the more I like it, to the extent that I feel it would benefit 3DNA users by eliminating its dependence on a third-party utility program (pstoedit). Of course, if you have access to Adobe Illustrator, you can manipulate the EPS file directly.

Xiang-Jun Lu <3dna.lu@gmail.com>
Last modified: Tue Sep 4 08:09:37 2007