I am new to Rosetta. I downloaded to my Mac and tried to build, following https://new.rosettacommons.org/docs/latest/getting_started/Getting-Started#introductory-rosetta-tutorials_installation-on-mac-linux. This says that there should be a directory main/source, however I don't have it:
(rosetta) mac% pwd
/Users/davidjaffe/software/rosetta/PyRosetta4.Release.python39.mac.release-318
(rosetta) mac% find . -name main -print
(rosetta) mac%
Any ideas what I'm doing wrong?
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The "main" directory is the main directory of Rosetta. Depending on how you installed it, you may have changed the name (or it was changed for you). The "main" directory is the directory which has the source/, database/, tests/, tools/ and demos/ directories.
But that's for the regular Rosetta download. The PyRosetta download doesn't contain most of that. Additionally, the process for building and installing PyRosetta into your Python interpreter is different than building and installing "plain" Rosetta for use as a command line program. Most of https://new.rosettacommons.org/docs/latest is based off of the command line Rosetta. While there are things there which are useful for PyRosetta, you will often have to "translate" from a command line context into a Python context.
But installation is a big difference - one for which there isn't a simple translation - and for instructions about installing PyRosetta, see the PyRosetta specific documentation at https://www.pyrosetta.org/
Thank you! The release directory that I was told to use is http://graylab.jhu.edu/download/PyRosetta4/archive/release. It has three flavors of download: MinSizeRel, Release and Debug. I downloaded the latest versions of the latter two for the Mac. However neither contains any of the directories you listed for rosetta, although a couple are present for pyrosetta:
So I'm baffled!
Rosetta proper is a set of C++ compiled command line programs. Much of the documentation you see for "Rosetta" (including the docs/ wiki you originally pointed to) is for the standard compiled, command line programs. All of these programs are (basically) a rather thin wrapper around the central Rosetta library.
PyRosetta is a Python-based wrapper around this central C++ library. (Basically, it's Python-level accessor functions to the compiled Rosetta library functions.) PyRosetta is used (and installed) differently from the standard command-line Rosetta programs, due to the fact that it's accessed through the Python interpreter.
The directories I mentioned (and the installation protocol that you originally linked to) is for the standard command line Rosetta. For installation instructions for PyRosetta, see the PyRosetta specific documentation at https://www.pyrosetta.org/downloads
You have downloaded PyRosetta. If you want to use the command line version, you can download it from https://www.rosettacommons.org/software/license-and-download -- Which one you want to download and install is dependent on how you want to use it. If you want to launch Rosetta from the command line, download regular, command line Rosetta. If you want to use it from within Python, download and install PyRosetta.
Note that you can have both regular Rosetta and PyRosetta installed on the same machine, (You can even have multiple versions of Rosetta & PyRosetta installed on the same machine, though to have multiple PyRosettas installed, you probably want to use a virtual environment system like Conda.)
Also note that unless you have special use cases, you probably want to be using the "Release" versions of either PyRosetta or Rosetta. The "debug" versions have extra checks enabled which help for figuring out problems with the Rosetta code, but which slow things down quite a bit.