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Last Updated: 2/8/18
This Mover computes which residues are lipid accessible and puts that information into the B-factors: 50 is lipid accessible, 0 is lipid INaccessible.
The Mover lives in main/source/src/protocols/membrane/.
Algorithm: First, it sets the B-Factor to zero for all atoms. Then it computes concave and outer hulls and goes through the slices. Residues that are on the boundary are lipid-exposed. If the angle between COM-CA-CB is smaller than the cutoff, then it is not lipid-exposed.
The following options are available within the RosettaScript interface:
angle_cutoff - Real - Provide the angle cutoff.
slice_width - Real - Provide the slice width.
shell_radius - Real - Provide the shell radius.
dist_cutoff - Real - Provide the distance cutoff.
tm_alpha - bool - Provide the tm_alpha.
| Flag | Description |
|---|---|
-mp::lipid_acc::angle_cutoff <Real> |
Cutoff for CA-CB-COM angle to identify lipid accessible residues, in degrees. < 90 faces towards COM, > 90 faces away from COM. Default = 65. For smaller proteins like GPCRs (number of spans <= 7), default = 45. |
-mp::lipid_acc::slice_width <Real> |
Width of the slice in Angstrom to compute hull. Default = 10.0. |
-mp::lipid_acc::shell_radius <Real> |
Radius of shell from outermost atoms that are still counted as boundary, i.e. how thick is lipid-exposed layer from the outside. Default = 6.0. |
-mp::lipid_acc::dist_cutoff <Real> |
Distances between boundary atoms longer than this cutoff (in 2D) will be cut in. Anything larger will be kept as boundary atoms. Default = 10.0. |
-mp::lipid_acc::tm_alpha <Bool> |
Is the main secondary structure in the membrane helical? Default = true. |
RosettaMP is described in