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:
cmd_mpscore_as-is.sh scores the protein as-is with respect to the fixed membrane cmd_mpscore_transform.sh transforms the protein first into the membrane before scoring cmd_mpscore_transform_optimize.sh 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:
cmd_mpscore_as-is.sh cmd_mpscore_transform.sh cmd_mpscore_transform_optimize.sh
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:
./visualize_clashes.py -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