Rosetta v2.0
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Thank you for downloading the Rosetta software. Component files for each 
Rosetta module can be found in the module-specific directory (e.g. Rosetta
Abinitio).  Each module shares source code located in the rosetta++ directory
and data files in the rosetta_database directory.  Each module directory 
contains a setup script (setup.bash) that should be executed to properly link 
each module to the shared components.

The source code can be compiled with 'make gcc'.  Because Rosetta still uses 
static memory allocation, you may encounter problems that require parameter
values defined in param.cc to be edited and the code recompiled. See module-
specific READMEs for any recommended parameter values.

In addition to functionalities associated with particular modules, the 
Rosetta binary can be used to 'score' structure according to the Rosetta
energy function using the '-score' command line option. A typical use to
score a single structure would use the command line:

rosetta.gcc -score -s <pdb_file> -scorefile <score_file>

Where <pdb_file> is the structure to be scored and <score_file> is an output 
file where scoring terms will be written.  To score a list of structures, use

rosetta.gcc -score -l <list_file> -scorefile <score_file>

where <list_file> contains a list of pdb files, one per line.

The '-score' mode can also be used to add sidechains to a structure by 
specifying that a structure should be output:

rosetta.gcc -score -s <pdb_file> -scorefile <score_file> -nstruct 1 -fa_output

where "-nstruct 1" indicates that a structure should be output and "-fa_output"
indicates that the structure should have fullatom sidechain coordinates.
If you want to keep any available sidechain coordinates on the input pdb file,
add "-fa_input" to the command line.  Command line options are listed and 
briefly explained in rosetta++/README.