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Prime Membrane Setup Panel |
This panel is used to set up an implicit membrane model for Prime refinement calculations.
To open the Prime Membrane Setup panel, you can:
Click Set Up Membrane in the Options dialog box of any of the Prime refinement panels.
Click Set Up in the Induced Fit Docking panel.
The implicit membrane is a slab-shaped region with a low dielectric constant, similar to the implicit solvent region. The low dielectric constant removes the penalties incurred by hydrophobic groups in the solvent region, and also removes the rewards gained by hydrophilic groups in the solvent region.
The membrane is marked in the Workspace by a semitransparent cube with a white line that is perpendicular to the surfaces of the membrane (which are planar). The membrane surfaces are colored red, and the other faces of the cube (which are interior to the membrane) are colored green. You can control whether the sides of the cube are displayed with the Show cube sides option. The direction of the line shows the orientation of the membrane.You can adjust both the thickness and the orientation of the membrane.
The implicit membrane model is intended for use with proteins that span the membrane. The slab is trimmed for efficiency, so that any structure that is too small or too far away from the membrane is likely to result in too much trimming and might not produce useful results.
If the protein has pockets that would be occupied by solvent (water), you can select these regions to exclude from the implicit membrane using the tools in the Region to exclude from membrane section. The solvent dielectric constant is then used for these excluded regions.
This section provides tools for initial placement of the membrane. The orientation and thickness of the membrane is indicated in the Workspace by a cube and a white line that is perpendicular to the plane of the membrane.
Load a membrane from the entry that is selected in the Project Table. The membrane is placed at the same location in space as in the source entry, so you should ensure that the protein in the source entry and the current entry are properly positioned.
If you have a structure from the OPM database, click this button to place the membrane according to the information stored with the structure. If you click this button without having an OPM structure, the membrane is placed symmetrically on the z axis.
Click this button to place the membrane so that the atoms given by the expression in the ASL text box are inside the membrane. The ASL expression can be entered in the text box, or you can click Select to specify the atoms in the Atom Selection dialog box, or click Set to Helices to use the secondary structure assignment to select the helices for placement inside the membrane.
ASL expression for the atoms to place inside the memrane. You can type an expression into this text box directly, or use the Select or Set to Helices buttons to enter an expression.
Opens the Atom Selection dialog box, so you can define the atoms to place inside the membrane.
Set the expression in the ASL text box to res.sec helix. This expression selects all residues for which the secondary structure assignment is to a helix, and requires that a secondary structure assignment has been made (e.g. with Tools → Assign Secondary Structure).
This section provides tools for adjusting the membrane position and thickness.
Use the text box and arrow buttons to adjust the thickness of the membrane. You can enter text into the text box. The arrow buttons perform fine adjustments, at the 0.1 Å level.
Select this option to adjust the position of the membrane. You can then rotate and translate the membrane in the same way as you do with structures, using the middle and right mouse buttons. When you have finished, deselect this option to resume normal Workspace operations.
Select this option to show the sides of the cube that defines the membrane. The location of the sides is not significant, it is only an aid to visualizing the membrane location.
In this section you can set up regions to be excluded from the membrane that are considered to be solvent-occupied regions in the protein. The solvent dielectric constant is used in these regions.
Select this option to pick atoms in the Workspace on which exclusion spheres will be placed, or for which you want to change the radius. The spheres are displayed in semitransparent green in the Workspace. The spheres should cover the region to be excluded from the membrane, and may overlap the protein. Picking an atom that has a sphere allows you to change the radius or to delete the sphere.
Set the radius of the selected sphere. This radius is also applied to newly placed spheres. The exact radius is not important, as long as the overlapping spheres cover the exclusion region.
Delete the current sphere.
Delete all exclusion spheres.
Add the membrane to the entries that are selected in the Project Table. The membrane is stored as a set of coordinates, for each end of the white line. The entries that you select should therefore contain proteins that occupy approximately the same region of space as the protein used to define the membrane. Otherwise, you will have to adjust the membrane location for these entries.
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