Download and Installation

1. Get the academic license for Rosetta at https://els.comotion.uw.edu/express_license_technologies/rosetta
2. Immediately, you will get the download link from Rosetta Commons by email.
3. Download and compile Rosetta. An MPI compiled version is needed for the RASREC and autoNOE protocols.
4. Download and install TALOS-N from http://spin.niddk.nih.gov/bax/software/TALOS-N/ (optional, the toolbox installer will otherwise do this for you automatically).
5. Download the VALL database (optional, the toolbox installer will otherwise do this for you automatically).
6. Download the CS-Rosetta toolbox and from within /csrosetta3/ (or /csrosetta3/com/ ), use the command "python install.py"

A tutorial on downloading and installing the toolbox, as well as setting up a run using the autoNOE protocol, is included in the following slides:
http://csrosetta.chemistry.ucsc.edu/sites/default/files/tutorials/Settin...

You may wish to include addition flags for your installation. For example:
./install.py -talos_dir ~/talos-N/ -rosetta ~/rosetta/main/source/bin/ -rosetta_database ~/rosetta/main/database/ -vall ~/CSROSETTA/csrosetta_vall.2008.apr24/

7. Test CS-Rosetta fragment picking:
source com/init
pick_fragments -cs tutorials/inputs/SgR145.tab

A note about fragment picking:
There is a talos-related bug that will consistently create an error:
"ERROR: Can't identify secondary structure file type (needs vertical psipred_ss2 or talos+ pred.ss): [target_name].fasta.talos/predSS.tab"

Until we resolve this, proceed as follows:
1) Open the predSS.tab file that has been created in the folder [target_name].fasta.talos/predSS.tab
2) Insert a line at the very top that says "REMARK TALOS-N"
3) Resubmit your pick_fragments command on the command line. The fragment picker will pick up where it left off.