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###                                                                                                                  ###
###       Two-component docking protocol                                                                             ###
###       The version of the tcdock executable used in this study, and in this example, is                           ###
###       available upon request.  The latest version can be obtained through the Rosetta GitHub                     ###
###       code repository.                                                                                           ###
###                                                                                                                  ###
###       Accurate design of coassembling multi-component protein nanomaterials                                      ###
###       King NP, Bale JB, Sheffler W, McNamara DE, Gonen S, Gonen T, Yeates TO, Baker D                            ###
###       Nature 2014, Supplementary Data                                                                            ###
###                                                                                                                  ###
###       Run the command lines below for an example of the docking protocol used for the T32 designs.               ###
###       -The trimer.pdb file contains a single subunit from PDB ID 3N79 biounit 1 prepared as described in         ###
###        the Supplementary Information                                                                             ###
###       -The dimer.pdb file contains a single subunit from PDB ID 3GFA biounit 1 prepared as described in          ###
###        the Supplementary Information                                                                             ###
###       -This same protocol can be executed on other input scaffolds and with different symmetries by changing     ###
###        the input PDB files and the corresponding tcdock::T3 and tcdock::T2 options to match the symmetry of      ### 
###        scaffolds and the desired symmetric architecture.  In the case of the T33 architecture, U1 and U2 are     ###
###        used instead of the tcdock::T3 and tcdock::T2 options.                                                    ###
###       -Other differences between the docking protocols used for the T32 and T33 designs in this study are noted  ###
###        in the input.flags file.                                                                                  ###
###                                                                                                                  ###
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path_to_tcdock_executable -database path_to_rosetta_database -tcdock::reverse false -tcdock::T3 trimer.pdb -tcdock::T2 dimer.pdb @input.flags
path_to_tcdock_executable -database path_to_rosetta_database -tcdock::reverse true -tcdock::T3 trimer.pdb -tcdock::T2 dimer.pdb @input.flags
