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 STRUCTURE PREDICTION

Follow the steps below. Example inputs and outputs are provided in the respective folders.

1) Adjust the paths for the Rosetta executable and database in the cmd_model_tmhelix.sh script

2) Run the script:

./cmd_model_tmhelix.sh

3) Examine the output and compare it to the provided one. It is always recommended to visualize the protein with respect to the membrane bilayer. Example scripts for this are provided in the 006_mp_visualize folder.

Note that in PyMOL line or stick representation, the membrane residue can show up as straight connecting lines between the individual virtual atoms. This artifact can be safely ignored.