General notes

Rosetta is used by a number of modules in Phenix including rosetta_refine, ERRASER and MR_rosetta. Installing Rosetta for rosetta_refine involves compiling some more programs for the interface between Phenix and Rosetta. The other programs will run with a binary installation of Rosetta or the compiled installation of Rosetta. From a practical point-of-view, making the effort to install the compiled version of Rosetta means that you can run all three programs.

To run any Rosetta programs, you need to install Rosetta from the Baker laboratory at the University of Washington. Once you have installed Rosetta you need to set the environmental variable $PHENIX_ROSETTA_PATH, $ROSETTA_BIN and $ROSETTA3_DB.

You will need the 2016.02.58402 bundle. It is quicker to download the source bundle and the binaries are not required when installing for ALL programs.

NOTE: If trouble...see the FULL INSTRUCTIONS at https://www.rosettacommons.org/support

Proceed with the following.

• go to https://c4c.uwc4c.com/express_license_technologies/rosetta, find "Academic License" and click on "LICENSE". Fill out the form, and receive by email a link to the download site and a login/password.
• Go to the latest download (for example Rosetta 2014.30) on the download site, select Download, and download Rosetta "as one bundle".
• Unpack and install Rosetta: Go to the directory where you want to install it and move the downloaded file (something like rosetta_src_2016.02.58402_bundle.tgz) there. Then...changing the names to match your bundle...

tar xzf rosetta_src_2016.02.58402_bundle.tgz

This should give you a directory like rosetta_src_2016.02.58402_bundle that contains:

demos main tools

• Now you want to compile. You must have python on your machine...if not you will need to install it from http://www.python.org/. You will also need scons. If you don't have scons you can get it from www.scons.org/. NOTE: you will need version 2.2 or later of python and 0.96.1 of scons. You can check your versions with:

python --version
scons --version

• NOTE 2: on Ubuntu you may also need zlib1g-dev. You can get this library and scons with:

sudo su   # UBUNTU ONLY FOR INSTALLING zlib1g and scons
apt-get install zlib1g-dev
apt-get install scons

In the scons command below the "-j2" means use 2 processors....adjust for your system. Takes about 1 hour with 2 processors. Please note: Do not move your Rosetta installation after compiling it. The compilation builds in path names, and if you move the binaries to some other place it will not run.

cd rosetta/main/source/
./scons.py -j2
cd ..

If you get to "scons: done building targets." you are all set!

• Notice where you have installed rosetta. The directory you just set up, now containing "main" is to be called "PHENIX_ROSETTA_PATH". Now you can now set a local environmental variable in your ".profile" (sh or bash shell) or ".cshrc" (c-shell) to mark where rosetta is located: if you are using the bash or sh shells:

export PHENIX_ROSETTA_PATH=/your-path-to-rosetta-here/
export ROSETTA_BIN=$PHENIX_ROSETTA_PATH/main/source/bin
export ROSETTA3_DB=$PHENIX_ROSETTA_PATH/main/database

or sh (C-shell):

setenv PHENIX_ROSETTA_PATH /your-path-to-rosetta-here/
setenv ROSETTA_BIN $PHENIX_ROSETTA_PATH/main/source/bin
setenv ROSETTA3_DB $PHENIX_ROSETTA_PATH/main/database

• The final step is to build the interface for rosetta_refine. This is a similar step to the previous scons step so supply as many nproc as available on your machine.

rosetta.build_phenix_interface nproc=2

Specific notes

To use the fragment server and your machine is behind a firewall and there is a proxy server you need to go through, then if you use a .hhr file to download files from the PDB then you will need to specify your proxy server. You can use the following command to specify the proxy server (replacing it with YOUR proxy server).

If you are using the bash or sh shells:

export HTTP_PROXY=proxyout.mydomain.edu:8080

or sh (C-shell):

setenv HTTP_PROXY proxyout.mydomain.edu:8080

• Now you are completely ready to go with Rosetta in Phenix

NOTE: If trouble on ubuntu 11.04 or later...also see: http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104 (but just concerning basic.settings and options.settings modifications and using : scons bin mode=release cxx=gcc cxx_ver=4.5)