1st script (refinement) command line
------------------------------------
~/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -database <path_to_db> -in:file:s <input_pdb> -parser:protocol refine.xml -parser:script_vars  res_to_fix=<fix_list> -parser:script_vars pdb_reference=<input_pdb> -parser:script_vars cst_full_path=<cst_file> -parser:script_vars cst_value=<cst_val> @flags -overwrite


Command line variables
----------------------
1. path_to_db: path to rosetta database
2. input_pdb: the input structure/model in pdb formant only
3. fix_list: a list (number and chain) of all residues to restrict to minimization separated by commas. Hypothetical Example: 1A,2A,3A,4A
4. cst_file: a file with the input coordinates of all CA atoms in the input_pdb. see example.cst and use make_csts.sh to make one.
5. cst_val: the coordinate constraint weight in the score function. PROSS default is 0.4


Before running a refinement job prepare a coordinate constraints file
---------------------------------------------------------------------
Command line to run make_csts.sh and save the output to a file:
make_csts.sh <input_pdb> >output_filename

Command line example
--------------------
~/Rosetta/main/source/bin/rosetta_scripts.default.linuxgccrelease -database ~/Rosetta/main/database/ -in:file:s input_example.pdb -parser:protocol refine.xml -parser:script_vars res_to_fix=1A,2A,3A,4A -parser:script_vars pdb_reference=input_example.pdb -parser:script_vars cst_full_path=example.cst -parser:script_vars cst_value=0.4 @flags -overwrite