Written by Frank Teets Last Modified Jun 21 2016

Table of Contents

Required Software

To productively use Rosetta, a number of additional programs are need:

    1. A text editor capable of outputting plain text files; For cmd-line tools, most people use Emacs, Vim, Nano, or similar. For GUI-based tools, Sublime Text and TextMate, are very good on mac and Gedit is included with Ubuntu Linux. Note that word processors like Microsoft Word and Libre/Open Office are unsatisfactory, as the additional formating they introduce will confuse Rosetta.
      1. A molecular viewing tool. Rosetta does not include a way to actually visualize the output files it creates; a tool such as PyMOL or Chimera is necessary to examine the output PDBs. Rosetta does include a PyMOLObserver for directly viewing its output in PyMOL; instructions for setting up PyMOLObserver are found here.
      1. A terminal. Unix and Apple users have suitable terminals installed by default. Windows users attempting to run Rosetta remotely on a Mac or Unix machine will require a tool like PuTTY to provide the necessary interface.

It may also help to familiarize yourself with the basics of command line interfaces. Particularly useful commands include:

ls foo          displays a list of files in the directory foo
cd foo          moves the current working directory to the directory foo
mv foo bar      moves all of foo into bar if bar is a directory or into a file called bar if not
cp foo bar      moves all of foo into bar if bar is a directory or into a file called bar if not
ln -s <path_to_bar> foo establishes a link called a symbolic link or symlink from foo to bar
top             lists the currently running processes, together with their process IDs. This is useful for how much computational resource your pro