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:

cmd_mptransform.sh cmd_mptransform_optimize.sh

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