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| Rosetta is a library based object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. | Rosetta is an object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions. |
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| The latest release of Rosetta, version 3.2, may be downloaded at http://www.rosettacommons.org/software. The software is free to academic users, who may get a license (and download link) by clicking on the appropriate link on the left side of the page. The user manual, containing more detailed installation and usage information, is available online at http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide. | For the tutorial, you can download binaries of Rosetta for: * Linux: [[attachment:rosetta_binaries_linux-mar7-11.tar.gz]] * Mac: [[attachment:rosetta_binaries_mac_mar7_11.tar.gz]] * Windows: ''Sorry. Not available'' |
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| Afterwards, please add the following two lines in your .bashrc file and do "source ~/.bashrc". Mac users should modify the lines accordingly. |
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| Rosetta is distributed as source code; individual applications must be compiled. Rosetta has been successfully built on the following platforms: | {{{ export ROSETTA3_SRC=/home/eman/eman2011/rosetta/rosetta_binaries_linux export ROSETTA3_DB=/home/eman/eman2011/rosetta/rosetta_database }}} |
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| Fully Support Platforms (extensively tested): • Darwin Kernel Version 9.6.0: root:xnu-1228.9.59~1/RELEASE_I386 i386 • Darwin Kernel Version 9.5.2: root:xnu-1228.8.59~2/RELEASE_I386 i386 • Linux 2.6.27-9-generic #1 SMP x86_64 GNU/Linux • Linux 2.6.10-1.741_FC3smp #1 SMP i686 athlon i386 GNU/Linux • Linux 2.6.9-78.0.8.ELsmp #1 SMP Wed i686 i686 i386 GNU/Linux |
For installation of the standard release, the latest release of Rosetta, version 3.2, may be downloaded at http://www.rosettacommons.org/software. The software is free to academic users, who may get a license (and download link) by clicking on the appropriate link on the left side of the page. The user manual, containing more detailed installation and usage information, is available online at [[http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide]]. |
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| Partial Support (built but limited testing was performed) • Fedora Core Linux v3 or greater, x86, 32-bit, GCC 4.0 (*)(**) • RedHat Enterprise Linux v3 or greater, x86, 32-bit, Intel C++ 9.1 (*) • RedHat Enterprise Linux v3 or greater, x86, 32-bit, GCC 4.0(**) • MinGW on Microsoft Windows XP, 32-bit, GCC 3.4 |
More details about the installation can be found at: [[attachment:Installation_Guide.pdf]] |
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| After downloading Rosetta, the next step is building the Rosetta executables. Rosetta uses 'scons' as its build system; a local version of scons is included in the Rosetta distribution. This does require Python version 2.2 or greater is installed. To use this version of Scons, call the file external/scons-local/scons.py within your Rosetta installation as your SCons executable. | Tutorial data is here: [[attachment:rosetta_tutorial_data.tar]] |
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| For the following build commands you need to be in the home directory of Rosetta source. In order to build a release version of Rosetta executables, simply run scons: Release Mode --This command will build the defaults: libraries devel, protocols, core, numeric, utility and all applications listed in src/apps.src.settings or src/pilot_apps.src.settings.all. scons bin mode=release Debug Mode -- In order to build a debug version of executables, remove the flag 'mode=release'. scons bin To display more rosetta-specific build options call scons -h Automatic location of other compilers (assuming they are already in your path) such as Intel C/C++ may be enabled by uncommenting the "program_path" line in 'tools/build/user.settings'. After running 'scons', links to executables are placed in the folder 'bin/'. Rosetta is run through the command line, with simulation parameters controlled through command line parameters, or (optionally) a flags file. Options can be listed with the command. Options, and arguments to the options, are separated by whitespace. A colon is used to clarify options when there are multiple separate options with the same name. Multiple layers of colons may be needed. fixbb.macgccrelease -in:file:s myinput.pdb -database mypath Options can also be written in a flag file. In this file, put one option on each line, still using the colon to specify the layers. An example options file appears below. -database /home/yiliu/Programing/branches/rosetta_database -in:file:s 1l2y_centroid.pdb -in:centroid_input -score:weights centroid_des.wts If this file were called “option”, then it would be used like this (notice the @ symbol): fixbb.macgccrelease @option Options are program-specific. For the options, one may find more information in two places: first the application documentation (http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide/); second, if you pass -help as a flag on the command line, Rosetta will spit out all existing options and then quit (ignoring other flags). You can download data ... [[attachment:rosetta_demo_2011.tgz]] ... etc. |
Tutorial documentation is here: [[attachment:Rosetta_Density_Tutorial.pdf]] (though this will also be handed out at the workshop, and may be updated before thursday) |
Rosetta
Thursday PM Practical
Rosetta is an object-oriented software suite which provides a robust system for predicting and designing protein structures, protein folding mechanisms, and protein-protein interactions.
For the tutorial, you can download binaries of Rosetta for:
Windows: Sorry. Not available
Afterwards, please add the following two lines in your .bashrc file and do "source ~/.bashrc". Mac users should modify the lines accordingly.
export ROSETTA3_SRC=/home/eman/eman2011/rosetta/rosetta_binaries_linux export ROSETTA3_DB=/home/eman/eman2011/rosetta/rosetta_database
For installation of the standard release, the latest release of Rosetta, version 3.2, may be downloaded at http://www.rosettacommons.org/software. The software is free to academic users, who may get a license (and download link) by clicking on the appropriate link on the left side of the page. The user manual, containing more detailed installation and usage information, is available online at http://www.rosettacommons.org/manuals/archive/rosetta3.2_user_guide.
More details about the installation can be found at: Installation_Guide.pdf
Tutorial data is here: rosetta_tutorial_data.tar
Tutorial documentation is here: Rosetta_Density_Tutorial.pdf (though this will also be handed out at the workshop, and may be updated before thursday)