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.
KEYWORDS: MEMBRANES ANALYSIS
Follow the steps below. Example inputs and outputs are provided in the respective folders. Three different options are provided for variable flexibility:
cmd_mptransform.sh transforms the protein into the membrane cmd_mptransform_optimize.sh 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