Installation

Rosetta is software from the Baker laboratory at the University of Washington https://www.rosettacommons.org. Rosetta is used by a number of modules in Phenix

• phenix.erraser
• phenix.mr_rosetta
• phenix.simple_homology_model.
• phenix.rosetta_refine

phenix.rosetta_refine requires a compilation of Rosetta from source as it requires some programs for the interface between Phenix and Rosetta that are not in the binary distribution. The first three 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 phenix Rosetta dependent programs.

Once you have installed Rosetta you need to set the environmental variable $PHENIX_ROSETTA_PATH.

Installation - Using standard Phenix installation

To use the latest Rosetta version, Phenix needs to be compiled using a compiler that is c++11 compatible. This is now the case from Phenix 1.14 and beyond. Users of macOS should use the command-line installer and install XCode to get the compilers.

Currently, there is an issue with using phenix.rosetta_refine and macOS High Sierra (10.13). The rosetta.run_tests step in the installation instructions is generating large files and using large amounts of memory.

Proceed with the following.

• Go to the Rosetta licensing website, 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. Then you can download Rosetta from the main Rosetta Commons website.
• You will need Rosetta version 3.9. It is quicker to download the source bundle. The binaries are not required when installing for ALL programs.
• Make the directory where you want to install Rosetta (if it does not already exist). Move the downloaded file (something like rosetta_src_2018.09.xxxxx_bundle.tgz) there. Then unpack the bundle...

% tar xzf rosetta_src_20??.??.?????_bundle.tgz (changing the names to
  match your bundle)

• You should have a directory like rosetta_src_2018.09.xxxxx_bundle that contains:

demos   main    tools

• The directory containing "main demo tools" 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/

or sh (C-shell):

%  setenv PHENIX_ROSETTA_PATH /your-path-to-rosetta-here/

• 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. If you installed Phenix in a location that requires administrative privileges (e.g. /usr/local on linux or /Applications on macOS), you will also need administrative privileges for building. NOTE: On linux, if you are using GCC 5.1 or later (Ubuntu 16.04 or later), there is an ABI change that requires an additional flag to allow linking between our CentOS 6 binary build and Rosetta. To apply this flag, copy this site.settings file to ${PHENIX_ROSETTA_PATH}/main/source/tools/build/site.settings before running this final step.

% rosetta.build_phenix_interface nproc=2

You should now be completely ready to go with Rosetta in Phenix that can be tested using

% rosetta.run_tests

Troubleshooting

• See FULL INSTRUCTIONS at https://www.rosettacommons.org/support
• Build may also be called with ./scons.py bin mode=release -j4
• Build may fail because it is unable to find the g++ requested by build. This can be fixed in two ways
  1. If you have the correct version of g++ installed, but it is not called by the name expected by the build, simply set a soft link from g++ to e.g. g++-4.6
  2. See: http://morganbye.net/blog/2011/05/rosetta-32-ubuntu-1104 for how to edit to tools/build/basic.settings and tools/build/options.settings and using "scons bin mode=release cxx=gcc cxx_ver=4.5"
• Build may fail due to shallow warnings. Edit tools/build/basic.settings to comment out all "warn" flags for your operating system.

Proxy Server Setup

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