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: scores the protein as-is with respect to the fixed membrane transforms the protein first into the membrane before scoring transforms the protein first into the membrane, optimizes the embedding with the high-resolution score function and then scores the protein

1) Adjust the paths for the Rosetta executable and database in the cmd_mpscore<...>.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:

pymol .pdb .pdb visualize_membrane.pml

The score files are given in the respective output folders.

4) You can visualize clashes via:

./ -p output_score_transform_optimize/4P79_A_0001_transform_optimize.pdb -r

The -r option visualizes the repulsive score term. The script writes a PyMOL script visualize_clashes.pml that can be run inside PyMOL after loading the structure file. To do this, run the following in a command line terminal:

pymol output_score_transform/4P79_A_0001_transform.pdb visualize_clashes.pml