The scripts and input files that accompany this demo can be found in the demos/protocol_captures directory of the Rosetta weekly releases.

This is a protocol capture, and represents the protocol at a fixed point in time. It may not work with the current version of Rosetta.


Follow the steps below. Example inputs and outputs are provided in the respective folders. Three different options are provided for variable flexibility: transforms the protein into the membrane transforms the protein into the membrane and optimizes the embedding with the high-resolution membrane score function

1) Adjust the paths for the Rosetta executable and database in the cmd_mptransform<...>.sh scripts. Make sure you understand the options in the cmd files.

2) Run the scripts:

3) Check your output: visualize the positions of the input and output structures in PyMOL with the visualize_membrane.pml script using the command line

pymol .pdb visualize_membrane.pml