Prime Membrane Setup Panel
This panel is used to set up an implicit membrane model for Prime refinement calculations.
To open this panel, click Set Up Membrane in any Prime panel that has this button. For example, open the Calculate Energy Panel, click Options, select Implicit membrane, and click Set Up Membrane.
- Using
- Features
- Additional Resources
Using the Prime Membrane Setup 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.
To adjust the membrane position manually:
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Select Adjust membrane position.
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Use the middle mouse button to rotate the membrane and the right mouse button to translate the membrane.
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Adjust the thickness by entering a value in the text box or using the arrow buttons to adjust the thickness up or down by 0.1 Å at a time.
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Deselect Adjust membrane position to return to normal Workspace operations.
To define excluded regions (solvent pockets) in the membrane:
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To define a region, select Place or edit exclusion spheres and pick atoms in the Workspace that are adjacent to the region. For each pick a sphere is placed on the atom.
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To adjust the volume of one or more spheres, pick the spheres in the Workspace, and use the Radius slider. This slider only uses integer values, because the exact size of the sphere isn’t critical: the spheres only have to cover the excluded region.
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To delete a sphere, pick the sphere and click Delete Current Sphere.
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When you have finished, deselect Place or edit exclusion spheres.
Prime Membrane Setup Panel Features
- Place Membrane section
- Adjust Membrane section
- Exclude region from membrane section
- Save to Selected Entries button
- Place Membrane section
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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 from Selected Entry button
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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.
- Place on an OPM Structure button
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If you have a structure from the OPM database (http://opm.phar.umich.edu), 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.
- Place by ASL button
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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 text box
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ASL expression for the atoms to place inside the membrane. You can type an expression into this text box directly, or use the Select or Set to Helices buttons to enter an expression. Once the membrane is placed, you can modify the ASL expression to adjust the position of the membrane.
- Select button
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Opens the Atom Selection Dialog Box, so you can define the atoms to place inside the membrane. You can reopen this dialog box after placing the membrane to make adjustments to the ASL expression and hence to the membrane position. If the previous ASL expression is not automatically loaded, use the Previous button to recall it. You can then make changes to the expression.
- Set to Helices button
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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 Edit → Assign → Secondary Structure).
- Adjust membrane section
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This section provides tools for adjusting the membrane position and thickness, once you have made an initial placement.
- Thickness text box and arrow buttons
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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.
- Adjust membrane position option
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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 mouse buttons. When you have finished, deselect this option to resume normal Workspace operations.
- Show cube sides option
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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.
- Exclude region from membrane section
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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. Excluded regions are defined by a set of spheres that are placed on atoms adjacent to the region. The spheres can overlap, and should cover the entire excluded region. It does not matter that they overlap the protein, because the protein dielectric is not affected.
- Place or edit exclusion spheres option
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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.
- Radius slider
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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 Current Sphere button
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Delete the current sphere.
- Delete All Spheres button
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Delete all exclusion spheres.
- Save to Selected Entries button
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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.