The AddMembraneMover initializes RosettaMP by configuring data needed for membrane representation. This mover is required for membrane protein modeling in Rosetta and must be called first. The AddMembraneMover adds the membrane residue to the Pose, sets up a default FoldTree, and initializes the MembraneInfo object. The correct setup of the root in the FoldTree for either a fixed membrane and movable protein or movable membrane and fixed protein is the responsibility of the protocol developer.
The following options are available within the RosettaScript interface:
spanfile - String - Provide the spanfile name.
anchor_rsd - Integer - The residue number in the pose to which the membrane residue should be anchored at.
membrane_rsd - Integer - The residue number that the membrane residue should have in the pose.
thickness - Float - Half of the desired membrane thickness.
steepness - Float - The steepness of the function describing the interface, the higher the steeper the transition. Ideally between 2 and 10.
center - Float - Desired center of the membrane bilayer.
normal - Float - Desired normal of the membrane bilayer.
include_lips - Boolean - To include a lips file for lipophilicity.
lipsfile - String - Provide the lipsfile name.
| Flag | Description |
|---|---|
-mp::setup::spanfiles <spanfile> |
AddMembraneMover only uses the first spanfile. Not a requirement if a structure is given that is transformed into membrane coordinates: use spans_from_structure flag in this case. |
-mp::setup::spans_from_structure <bool> |
If no spanfile is given, the user has the option of creating a SpanningTopology object from the given structure. Structure must be transformed into membrane coordinates. Spanfile is written with this option: out.span |
-mp::setup::lipsfile <lipsfile> |
Read in user-provided lipsfile if initializing from Command Line. Defaults to "mypdb.lips4" |
-mp::setup::membrane_rsd <residue number for MEM residue> |
optional; read in user-provided membrane residue position. Default to the MEM residue from previously generated framework PDB. |
-mp::setup::center <three real numbers defining the center point> |
optional; user can provide desired membrane center coordinate. |
-mp::setup::normal <three real numbers defining the normal vector> |
optional; user can provide desired membrane normal vector. |
-mp::thickness <Real> |
One-half thickness of the membrane used by the high resolution scoring function. Overwrites default thickness of 15A (membrane is 30A thick). |
-mp::membrane_core <Real> |
Set membrane core thickness for Lazaridis-Karplus. Default is 15A, ie (-15, 15). |
-mp::steepness <Real> |
Control transition region between polar and nonpoar phases for the membrane model used by the high resolution energy function. Default = 10 gives a 6A transition region. |
Alford RF, Koehler Leman J, Weitzner BD, Duran A, Tiley DC, Gray JJ (2015). An integrated framework advancing membrane protein modeling and design. PLoS Comput. Biol. - In Press