{"id":2482,"date":"2019-02-25T16:44:36","date_gmt":"2019-02-25T16:44:36","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf3\/?page_id=2482"},"modified":"2025-06-19T17:58:44","modified_gmt":"2025-06-19T16:58:44","slug":"phenix-rosetta","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf3\/software\/applications\/phenix-rosetta\/","title":{"rendered":"Phenix and Rosetta Commons"},"content":{"rendered":"

Overview<\/h2>\n

Phenix is a software suite for the automated determination of macromolecular structures using X-ray crystallography and other methods. Versions 1.16 & 1.14 are available on the CSF.<\/p>\n

Rosetta Commons is a library-based object-oriented software suite which provides a system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. Version 2018.33 (3.10) is available on the CSF.<\/p>\n

Phenix and Rosetta are often used together.<\/p>\n

Restrictions on use<\/h2>\n

There is no access to any source code for Phenix and Rosetta on on the CSF.<\/p>\n

All users must abide by the license agreements which can be viewed here:<\/p>\n

Phenix License<\/a>
\nRosetta Commons License<\/a><\/p>\n

The licenses are also available in the installation directories along with appropriate copyright noitces.<\/p>\n

Who may use Phenix and Rosetta?<\/h3>\n

Staff and students of The University of Manchester. Visitors are not permitted access to this software.<\/p>\n

The software may only be used at The University of Manchester.<\/p>\n

What may Phenix and Rosetta be used for?<\/h3>\n

You are permitted to use Phenix and Rosetta only<\/strong> for not-for profit academic research purposes.<\/p>\n

What may Phenix and Rosetta not be used for?<\/h3>\n

The software must not<\/strong> be used for:<\/p>\n

    \n
  1. research, consultancy or services, leading to commercial exploitation of the software, including any fee-based service project, or<\/li>\n
  2. any purpose which leads to it being commercially exploited by the employer of students on industrial placement or part-time courses.<\/li>\n<\/ol>\n

    You may not copy or distribute the software.<\/p>\n

    How should the program be cited?<\/h3>\n

    You must make results generated using the software available to other academic researchers. Typically, this is done via publication. In all instances you should cite the software appropriately as per the guidance on the software developers websites:<\/p>\n

    Phenix Citation Information.<\/a>
    \n    Rosetta Citation Information.<\/a><\/p>\n

    Risks<\/h3>\n

    You are required to discuss anything that is unclear about your usage and the license with your line management in the first instance to obtain further guidance.<\/p>\n

    Requesting Access<\/h3>\n

    Please confirm by contacting us<\/a> that you have read the licenses and that your usage is within the conditions.<\/p>\n

    Set up procedure<\/h2>\n

    We now recommend loading modulefiles within your jobscript so that you have a full record of how the job was run. Alternatively, you may load modulefiles on the login node and let the job inherit these settings<\/abbr>.<\/p>\n

    To access the software you must first load either or both of the software modulefiles (depending on which apps you wish to use):<\/p>\n

    # Phenix modulefile (you must be in the phenix group to access this). Load only one of these versions:\r\nmodule load apps\/binapps\/phenix\/1.20\r\nmodule load apps\/binapps\/phenix\/1.18\r\nmodule load apps\/binapps\/phenix\/1.16\r\nmodule load apps\/binapps\/phenix\/1.14\r\n\r\n# Rosetta modulefile (you must be in the rosetta group to access this)\r\nmodule load apps\/binapps\/rosetta\/2020.08\r\nmodule load apps\/binapps\/rosetta\/2018.33\r\n<\/pre>\n
    Running the application<\/h2>\n
    Please do not run either applications on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
    However, it is possible to run the following command on the login node to get a list of Phenix executables that can be run from your jobscripts:<\/p>\n
    \r\nphenix.list | less\r\n<\/pre>\n
    The above command will show you a list of phenix executable names, a page at a time. Press space to advance to the next page and press q to exit from displaying this list.<\/p>\n
    You may also want to check the online Phenix Reference Manial<\/a> for a description of how to run the various tools. For example, to read about how to use phenix.refine<\/code> see here<\/a>.<\/p>\n
    In the job script examples below we use version 1.14, replace this with version 1.16 if you want to use the newer version.<\/p>\n
    Serial batch job submission<\/h3>\n
    An example for running phenix<\/code>, based on the supplied example data. Create a batch submission script, loading the version of the software you require:<\/p>\n
    #!\/bin\/bash --login\r\n#$ -cwd\r\n\r\n# Load the modulefile in the jobscript\r\nmodule load apps\/binapps\/phenix\/1.14\r\n\r\nphenix.refine $PHENIX\/examples\/rnase-s\/rnase-s.pdb \\\r\n  $PHENIX\/examples\/rnase-s\/rnase25.mtz xray_data.labels=FNAT,SIGFNAT,merged \\\r\n  xray_data.r_free_flags.generate=True ncs.type=torsion \\\r\n  refine.strategy=individual_sites+individual_sites_real_space+individual_adp+tls+occupancies \\\r\n  tls.find_automatically=True\r\n<\/pre>\n
    Submit the jobscript using:<\/p>\n
    qsub scriptname<\/em><\/pre>\n
    where scriptname<\/em> is the name of your jobscript.<\/p>\n
    Another example job script that runs rosetta<\/code><\/p>\n
    #!\/bin\/bash --login\r\n#$ -cwd\r\n\r\n# Load the modulefile in the jobscript (use the version you require)\r\nmodule load apps\/binapps\/rosetta\/2018.33\r\n\r\nfixbb -in:file:s \\\r\n$ROSETTA\/demos\/public\/domain_insertion\/rosetta_outputs\/AnchoredPDBCreator\/S_0001.pdb\r\n<\/pre>\n
    Submit the jobscript using:<\/p>\n
    qsub scriptname<\/em><\/pre>\n
    where scriptname<\/em> is the name of your jobscript.<\/p>\n
    Parallel batch job submission<\/h3>\n
    If the phenix tool you are running supports multi-core parallelism you can add the nproc<\/code> flag to the phenix command-line in the jobscript to set the number of cores. For example:<\/p>\n
    #!\/bin\/bash --login\r\n#$ -cwd\r\n#$ -pe smp.pe 8       # 2 to 32 cores permitted\r\n\r\n# Load the modulefile in the jobscript\r\nmodule load apps\/binapps\/phenix\/1.14\r\n\r\nphenix.refine $PHENIX\/examples\/rnase-s\/rnase-s.pdb \\\r\n  $PHENIX\/examples\/rnase-s\/rnase25.mtz xray_data.labels=FNAT,SIGFNAT,merged \\\r\n  xray_data.r_free_flags.generate=True ncs.type=torsion \\\r\n  refine.strategy=individual_sites+individual_sites_real_space+individual_adp+tls+occupancies \\\r\n  tls.find_automatically=True nproc=$NSLOTS<\/strong>\r\n                                       #\r\n                                       # $NSLOTS will be automatically set to the number of\r\n                                       # cores requested on the -pe line above.\r\n<\/pre>\n
    Submit the jobscript using:<\/p>\n
    qsub scriptname<\/em><\/pre>\n
    where scriptname<\/em> is the name of your jobscript.<\/p>\n
    The Rosetta installation is a binary<\/em> installation that does not contain any MPI (parallel) executables. If you are familiar with the MPI (parallel) executable and wish to run them, please contact us<\/a> to request an install of those executables.<\/p>\n
    Further info<\/h2>\n