Install CS-Rosetta Toolbox

2.0 Dependencies

The CS-Rosetta toolbox requires Python 2.7. The Python executable should be named python2.7.

2.1 Download

The CS-Rosetta toolbox is available under Downloads.

The fragment picking module of CS-Rosetta requires a significant amount of disk-space. You can install the tools without the fragment picker by using the option -nopicking. This is advisable if you use a desktop/laptop for pre- and post-processing, while you run fragment picking and simulations on a mainframe computer.

2.2 Unpack the Archive

tar -xvzf csrosetta_toolbox_ver1.0.tgz

which should produce output like this:


2.3 Run the installation script

The installation script is in the top-level toolbox directory and has to be run at least once for each installation.The installation script will perform several tasks:

  • generate init script: csrosetta3/com/init
  • integrate ROSETTA
  • integrate existing TALOS+ or TALOS-N or download from
  • download chemical shift VALL from here or use Rosetta's distribution available within rosetta_src/tools/fragment_tools/ folder of your Rosetta installation.
  • download BLAST executable from
  • download genome/nr database from

The installation script will look for TALOS+ or TALOS-N in the System-Path ($PATH). If TALOS+ or TALOS-N cannot be found, the required components from NMRPipe will be downloaded automatically if not disabled (-notalos).
BLAST, VALL and the genome/nr database are required for fragment picking and will only be installed if not disabled with option -nopicking. The script is able to resume broken downloads and can also be rerun at a later time
to check for any updates.
To run the installation:

cd csrosetta3 [-nopicking] [-notalos]

2.4. Update your profile

To use the CS-Rosetta toolbox you need to run the setup script csrosetta3/com/init once per shell-session. Ideally you manually edit your .bashrc or .cshrc and add the following line

#loading CS-Rosetta toolbox
source $HOME/csrosetta3/com/init

Replace $HOME/csrosetta3 by the path used for the toolbox installation. The init-script recognizes whether you have tcsh or bash as input shell and links the appropriate script com/init.bashrc or com/init.cshrc to com/init.




When I run the installation script of the CS-Rosetta Toolbox. There's a error in it. The information of the error is :

Cannot install frag-picker without valid ROSETTA installation
AUTO-DETECTION FAILED: cannot find ROSETTA binaries.
Run with -rosetta to point to binaries if toolbox is intended for automatic setup of CS-ROSETTA calculations
AUTO-DETECTION FAILED: cannot find ROSETTA database.
Run with -rosetta_database to point to database if toolbox is intended for automatic setup of CS-ROSETTA calculations

Do you have some methods or advise of how to solve this problem? Thank you!

You can add path to your rosetta installation manually by using
-rosetta /path_to_your_rosetta_binaries
-rosetta_database /path_to_your_rosetta_database

Open in a text editor and you can see other options such as Talos directory etc.

The installation script is written for linux installations, if you are setting up on a Mac, you'll need to manually edit file to correct the file names for rosetta binary files. And maybe edit file in frag_picker sub-directory after installation to make sure it find correct frag picker binary.

I have a problem too with the automatic detection of rosetta binaries using the csrosetta_toolbox_ver1.3.1.tgz file
Strangely when I use the fleg -rosetta, the binaries are not detected even if I point toward the correct folder. See below:

python2.7 -rosetta /home/quinte98/SOFTS_NMR/ROSETTA/rosetta3.3_bundles/rosetta_source/ -rosetta_database /home/quinte98/SOFTS_NMR/ROSETTA/rosetta3.3_bundles/rosetta_database/
AUTO-DETECTION FAILED: cannot find ROSETTA binaries.
Run with -rosetta to point to binaries if toolbox is intended for automatic setup of CS-ROSETTA calculations
Installation of CS-Rosetta Toolbox in path /home/quinte98/csrosetta3 ...
Generate init script...
ls: impossible d'accéder à ../com/*.com: Aucun fichier ou dossier de ce type

Nonetheless, the right path for the rosetta_database are correctly written in the init file. See below :

#the path to the ROSETTA installation (yields defaults for setup_run options -database and -binaries_prefix)
setenv ROSETTA3_DB /home/quinte98/SOFTS_NMR/ROSETTA/rosetta3.3_bundles/rosetta_database/

It's like the -rosetta flag doesn't work and the setenv ROSETTA3_BIN is not written in the init file.
How can I solve this ?



i have exactly the same problem as qunite98. I am using Ubuntu 10.4.

Thanks for any help,

As a solution to my problem, I made the installation with Rosetta3.4 in the default directories mentioned in the csrosetta installation protocol.
It works nice. Binairies are automatically detected.
It seems that it's a little bit complicated to use a previous version of rosetta.
Good luck.


Hi Quinte98 and pwurm,

the toolbox only works together with Rosetta3.4 + patch.
The autodetection makes sure that the correct version is present.
I'll see if I can improve the error-messages to make that point clearer.