| Flag | Description |
|---|---|
| -mp:setup:spanfiles <vector of strings> | Spanning topology file converted from OCTOPUS output; unless otherwise specified for certain applications, only one should be provided |
| -mp:setup:spans_from_structure <bool> | Uses spanning topology computed from the PDB; requires the protein to be transformed into the membrane coordinate frame! |
| -mp:setup:lipsfile <string> | Lipid accessibility file converted from LIPS output, default=mypdb.lips4 |
| -mp:setup:center <vector of reals> | Membrane center x,y,z |
| -mp:setup:normal <vector of reals> | Membrane normal x,y,z |
| -mp:setup:membrane_rsd <real> | Membrane residue number for reading in a PDB file with MEM coordinates |
| -mp:thickness <real> | User-defined membrane thickness. Overwrites default thickness of 60A. |
| -mp:scoring:hbond <bool> | Hydrogen bonding energy correction for membrane proteins |
| -mp:no_interpolate_Mpair <bool> | Advanced scoring parameter from RosettaMembrane; don't interpolate between layers for membrane pair potential |
| -mp:Hbond_depth_correction <bool> | Advanced scoring parameter from RosettaMembrane; correct hydrogen bonds for membrane depth |
| -mp:TMprojection <bool> | Advanced scoring: Penalty for hydrophobic mismatch on/off. |
| -mp:wt_TMprojection <real> | Advanced scoring: Weight for hydrophobic mismatch penalty. |
| -mp:non_helix <bool> | Advanced scoring: Penalty for non-helix residues in the membrane on/off. |
| -mp:wt_non_helix <real> | Advanced scoring: Weight for non-helix penalty. |
| -mp:termini <bool> | Advanced scoring: Penalty for termini in the membrane on/off. |
| -mp:wt_termini <real> | Advanced scoring: Weight for termini penalty. |
| -mp:secstruct <bool> | Advanced scoring: Penalty if structure-based secondary structure doesn\t match predicted one - on/off |
| -mp:wt_secstruct <real> | Advanced scoring: Weight for secondary structure penalty. |
| -mp:spanning <bool> | Advanced scoring: Penalty if structure-based spanning doesn\t match spanfile - on/off. |
| -mp:wt_spanning <real> | Advanced scoring: Weight for spanning penalty. |
| -mp:viewer:thickness <real> | PyMOL plugin: Thickness of membrane to visualize, default=15 |
| -mp:viewer:num_points <int> | PyMOL plugin: Number of points to define the membrane planes. x >= 3 |
| -mp:visualize:embedding <bool> | VisualizeEmbedddingMover: Visualize embedding centers and normals for each TMspan |
| -mp:visualize:spacing <real> | VisualizeMembraneMover: Spacing of virtual membrane residues representing the membrane planes, default=5 |
| -mp:visualize:width <real> | VisualizeMembraneMover: Width of membrane planes for n by n plane, default=100 |
| -mp:visualize:thickness <real> | VisualizeMembraneMover: Thickness of membrane to visualize, default=15 |
| -mp:visualize:plane_radius <real> | VisualizeMembraneMover: Radius of membrane planes to draw in PyMol - part of the PyMol viewer plugin |
| Flag | Description |
|---|---|
| -membrane | Initialize a pose as a membrane pose |
| -in:file:spanfile | Spanfile containing transmembrane span information, converted from OCTOPUS output |
| -in:file:lipofile | Lipophilicity file containing lipid accessibilities, converted from LIPS output |
| -center_search | Perform membrane center search, default false |
| -normal search | Perform membrane normal search, default false |
| -center_mag | Magnitude of membrane normal center search (Angstroms), default 1 |
| -center_max_delta | Magnitude of maximum membrane width deviation during membrane center search (Angstroms), default 5 |
| -normal_start_angle | magnitude of starting angle during membrane normal search (degrees), default 10 |
| -normal_delta_angle | magnitude of angle deviation during membrane normal search (degrees), default 10 |
| -normal_cycles | Cycles for finding good embedding normal, default 100 |
| -normal_max_angle | magnitude of maximum angle deviation during membrane normal search (degrees), default 40 |
| -normal_mag | Magnitude of membrane normal angle search (degrees), default 5 |
| -smooth_move_frac | ???, default 0.5 |
| -no_interpolate_Mpair | Don't interpolate between layers for pair interactions, default false |
| -Menv_penalties | Turn on penalties, default false |
| -Mhbond_depth | Membrane depth dependent correction to the hbond potential, default false |
| -Membed_init | ??? default false |
| -Fa_Membed_update | ??? default false |
| -fixed_membrane | Fix membrane position, by default the center is at [0,0,0] and membrane normal is the z-axis, default false |
| -membrane_center | Membrane center x,y,z |
| -membrane_normal | Membrane normal x,y,z |
| -thickness | One leaflet hydrocarbon thickness for solvation calculations (Angstroms), default 15 |
| -view | View membrane during protocol, default false |
| -debug | Print debug output, default false |
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