3DNA users' manual

The 3DNA package is command-line driven, much like Unix commands. Running each program with the -h option (e.g., find_pair -h) will provide you with detailed usage information. Once you are familiar with the package, it should be straightforward to combine the various pieces in a script to automate your tasks. The utility program blocview, a Perl script, illustrates this idea.

In the 3DNA v2.0 distribution, there is a users' manual, with technical details on the underlying algorithms for 3DNA analysis and rebuilding (which have mostly been taken from SCHNAaP/SCHNArP). Please also visit, and contribute if possible, to the 3DNA wiki pages.

Importantly, there is nothing more effective for learning and mastering 3DNA than to reproduce exactly and understand thoroughly the recipes reported in the 2008 NP paper. I stand firmly behind the reported results, and would be quick to address any difficulties you may experience at the 3DNA forum.