Outside links

The following links point to tools that are relevant to 3DNA.

  • Curves+ — an updated version of the well-known Curves program, and it conforms to the standard base reference frame.
  • SwS — a Solvation web Service for Nucleic Acids where 3DNA plays a role.
  • 3D-DART — 3DNA-Driven DNA Analysis and Rebuilding Tool. Another web-interface to commonly used 3DNA functionality.
  • do_x3dna — “do_x3dna has been developed for analysis of the DNA/RNA dynamics during the molecular dynamics simulations. It uses 3DNA package to calculate several structural descriptors of DNA/RNA from the GROMACS MD trajectory. It executes 3DNA tools to calculate these descriptors and subsequently, extracts these output and saves in to external output files as a function of time.”
  • Raster3D — a set of tools for generating high quality raster images of proteins or other molecules.
  • MolScript — a program for displaying molecular 3D structures, such as proteins, in both schematic and detailed representations.
  • Jmol — an open-source Java viewer for chemical structures in 3D with features for chemicals, crystals, materials and biomolecules.
  • PyMOL — a user-sponsored molecular visualization system on an open-source foundation.
  • RasMol — a program for molecular graphics visualisation originally developed by Roger Sayle. Note that v2.7.x has problem in displaying base block files in Alchemy format.
  • ImageMagick — a software suite to create, edit, compose, or convert bitmap images.
  • NDB — Nucleic acids database.
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