|The Rosetta++ software suite focuses on the prediction and design of protein structures, protein folding mechanisms, and protein-protein interactions. The Rosetta codes have been repeatedly successful in the Critical Assessment of Techniques for Protein Structure Prediction (CASP) competition as well as the CAPRI competition and have been modified to address additional aspects of protein design, docking and structure.|
- 3.4: /usr/local/rosetta3.4 (Mar 2012).
- 3.3: /usr/local/rosetta3.3 (Aug 2011).
- 3.2: /usr/local/rosetta3.2 (Mar 2011).
- 3.1: /usr/local/rosetta3.1 (Sep 2009).
Rosetta 3.5 Documentation
To run a set of demos, do the following:
[biowulf]$ qsub -I -l nodes=1 [p2]$ mkdir rosetta_demos [p2]$ cd rosetta_demos [p2]$ tar xzvf /usr/local/rosetta3.5/helix_demos_3.5.tgz [p2]$ ./run_demos.sh
The script run_demos.sh will run through common protocols, each taking no more than a few minutes to complete. The input and output will give a good idea on how to use Rosetta 3.x.
Rosetta v3.5 contains the same core libraries and algorithms as the version 2 series, but is significantly streamlined and simplified. The two major differences are:
- There are multiple executables to perform the different functionalities, rather than one monolithic executable
- Options and input can be encapsulated in a single 'flag' file, rather than given on the command line and in the paths.txt file
An easy way of selecting the version is to use modules. To see the modules available, type
module avail rosetta
To select a module, type
module load rosetta/[ver]
where [ver] is the version of choice. This will set your $PATH variable, as well as $ROSETTA_DATABASE.
The main Rosetta v3.5 executables are:
Performs de novo protein structure predictionIdentifies low free energy sequences for target protein backbonesPredicts the structure of a protein-protein complex from the individual structures of the monomer componentsScore a structure with the Rosetta energy functionRelaxes a structure into a minimal energy stateBuild and score internal loops for homology modelling
In addition, there are protocols for:
- comparative modeling
- enzyme design
- flexible peptide docking
- membrane abinitio folding
- symmetric docking
Fragment files can be generated locally using the make_fragments.pl script. This will generate three secondary structure predictions using SAM, Psipred, and Porter.
Fragment files can also be generated at the Robetta Server Site.
Supporting Programs and Scripts
Here are some supporting programs and scripts for streamlining certain tasks:
Manipulate input and output filesEvaluating Rosetta outputCluster decoys and models
Run as a batch job
Create a batch input file, e.g. 'rosettaRun':
#!/bin/bash #PBS -N rosetta #PBS -e rosetta.err #PBS -o rosetta.log cd $PBS_O_WORKDIR module load rosetta/3.5 relax @flags > relax.log
Submit this job using the PBS 'qsub' command. Example:
qsub -l nodes=1 rosettaRun
See here for more information about PBS.
Run as a swarm
Create a swarmfile, e.g. 'rosettaSwarm':
AbinitioRelax @flags -out:file:silent abinito1.out > abinitio1.log AbinitioRelax @flags -out:file:silent abinito2.out > abinitio2.log AbinitioRelax @flags -out:file:silent abinito3.out > abinitio3.log AbinitioRelax @flags -out:file:silent abinito4.out > abinitio4.log AbinitioRelax @flags -out:file:silent abinito5.out > abinitio5.log AbinitioRelax @flags -out:file:silent abinito6.out > abinitio6.log AbinitioRelax @flags -out:file:silent abinito7.out > abinitio7.log AbinitioRelax @flags -out:file:silent abinito8.out > abinitio8.log
Submit this job using the 'swarm' command. Example:
swarm -f rosettaSwarm --module rosetta/3.5
See here for more information about using swarm.
Run as an MPI batch job
The Rosetta executables have been compiled to utilize MPI. Not every executable can parallelize, but the basic abinitio works well. You will need to load a different module (mpi_*) instead of the default.
Create a batch input file, e.g. 'rosettaRunMPI':
#!/bin/bash #PBS -N rosettaMPI #PBS -e rosettaMPI.err #PBS -o rosettaMPI.log cd $PBS_O_WORKDIR module load rosetta/mpi_3.5 mpirun -np 96 -machinefile $PBS_NODEFILE AbinitioRelax @flags combine_silent -database $ROSETTA_DATABASE -in:file:silent silent_* -out:file:silent silent.out rm silent_*
The above is an example of a 96-cpu MPI job. You will need to allocate the proper number of nodes and cores to match this value. For example, 4 c24 nodes:
qsub -l nodes=4:c24 rosettaRunMPI
Or 6 c16 nodes:
qsub -l nodes=6:c16 rosettaRunMPI
NOTE:The number of decoys MUST be equal to or greater than the number of processors, as set by the -np option to mpirun. Otherwise the program will exit with errors.
cat_silent.pl: concatenate silentfiles
changeChain: change the chain id of a PDB
createLoop.pl: create a dummy structure from a sequence of amino acids
createTemplate.pl: create a homology model template from a FASTA file and a homologous structure
VMD: X-Windows molecular graphics viewer
getColumn.pl: display silentfile and scorefile columns
gnuplot: graphically display data
cluster_plot.pl: generate a gnuplot input file to plot the score versus another field
histogram.pl: generate a quick histogram from STDIN data
cluster_pdbs.pl: cluster a set of PDBs
cluster_variation.pl: find per-residue variation within a cluster