Rosetta is a software suite that includes algorithms for computational modeling and analysis of protein structures. It has enabled notable scientific advances in computational biology, including de novo protein design, enzyme design, ligand docking, and structure prediction of biological macromolecules and macromolecular complexes.
Availability and Restrictions
Versions
The Rosetta suite is available on Owens and Pitzer. The versions currently available at OSC are:
Version | Owens | Pitzer |
---|---|---|
3.10 | X | X |
3.12 | X* | X* |
You can use module spider rosetta
to view available modules for a given machine. Feel free to contact OSC Help if you need other versions for your work.
Access for Academic Users
Rosetta is available to academic OSC users. Please review the license agreement carefully before use. If you have any questions, please contact OSC Help.
Publisher/Vendor/Repository and License Type
Rosetta, Non-Commercial
Usage
Usage on Owens and Pitzer
To set up your environment for rosetta load one of its module files:
module load rosetta/3.12
Here is an example batch script that uses Rosetta Abinitio Relax application:
#!/bin/bash #SBATCH --job-name="rosetta_abinitio_relax_job" #SBATCH --ntasks=1 #SBATCH --time=0:10:0 #SBATCH --account=PAS1234 scontrol show job $SLURM_JOB_ID export module reset module load rosetta/3.12 module list echo $TMPDIR cd $TMPDIR mkdir input_files sbcast -p $ROSETTA3/demos/tutorials/denovo_structure_prediction/Denovo_structure_prediction.md $TMPDIR/Denovo_structure_prediction.md sbcast -p $ROSETTA3/demos/tutorials/denovo_structure_prediction/folding_funnels.png $TMPDIR/folding_funnels.png cd $ROSETTA3/demos/tutorials/denovo_structure_prediction/input_files/ for FILE in * do sbcast -p $FILE $TMPDIR/input_files/$FILE done cd $TMPDIR AbinitioRelax.linuxiccrelease @input_files/options ls -l sgather -pr $TMPDIR ${SLURM_SUBMIT_DIR}/sgather
Here is an example batch script that uses Rosetta MPI Docking script:
#!/bin/bash #SBATCH --job-name="rosetta_scripts_mpi_docking_job" #SBATCH --nodes=2 #SBATCH --time=0:10:0 #SBATCH --account=PAS1234 scontrol show job $SLURM_JOB_ID export module reset module load rosetta/3.12 module list sbcast -p ~support/share/reframe/source/rosetta/6shs_PIB.pdb $TMPDIR/6shs_PIB.pdb sbcast -p ~support/share/reframe/source/rosetta/pib-abeta.xml $TMPDIR/pib-abeta.xml sbcast -p ~support/share/reframe/source/rosetta/pib.params $TMPDIR/pib.params cd $TMPDIR srun rosetta_scripts.mpi -s 6shs_PIB.pdb -nstruct 100 -extra_res_fa pib.params -parser:protocol pib-abeta.xml -add_orbitals True -out:prefix t_ -out:pdb True sgather -pr $TMPDIR ${SLURM_SUBMIT_DIR}/sgather