{"id":368,"date":"2013-04-26T13:01:35","date_gmt":"2013-04-26T13:01:35","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=368"},"modified":"2019-02-25T16:48:42","modified_gmt":"2019-02-25T16:48:42","slug":"phenix_rosetta","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/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. Version 1.9 is available on the CSF.<\/p>\n

Rosetta 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 3.3 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

    Set up procedure<\/h2>\n

    To access the software you must first load either or both of the modulefiles:<\/p>\n

    \r\n# Rosetta modulefile\r\nmodule load apps\/binapps\/rosetta\/2015.19\r\n\r\n# Choose one of the following phenix versions\r\nmodule load apps\/binapps\/phenix\/1.14\r\nmoudle load apps\/binapps\/phenix\/1.9\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
    Serial batch job submission<\/h3>\n
    Make sure you have the modulefile loaded then create a batch submission script, for example (based on supplied example data):<\/p>\n
    \r\n#!\/bin\/bash\r\n#$ -S \/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n\r\n$PHENIX\/build\/intel-linux-2.6-x86_64\/bin\/phenix.refine $PHENIX\/examples\/rnase-s\/rnase-s.pdb \\\r\n$PHENIX\/examples\/rnase-s\/rnase25.mtz xray_data.labels=FNAT,SIGFNAT,merged \\\r\nxray_data.r_free_flags.generate=True ncs.type=torsion \\\r\nrefine.strategy=individual_sites+individual_sites_real_space+individual_adp+tls+occupancies 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:<\/p>\n
    #!\/bin\/bash\r\n\r\n#$ -S \/bin\/bash\r\n#$ -V\r\n#$ -cwd\r\n\r\n$PHENIX_ROSETTA_PATH\/main\/source\/bin\/fixbb.linuxgccrelease -in:file:s \\\r\n$PHENIX_ROSETTA_PATH\/demos\/public\/domain_insertion\/rosetta_outputs\/AnchoredPDBCreator\/S_0001.pdb\r\n\r\n<\/pre>\n
    Parallel batch job submission<\/h3>\n
    Given an example parallel jobscript, including suitable PE if applicable. If it does not run in parallel state that.<\/p>\n
    Further info<\/h2>\n