Set Up Membrane Dialog Box

In this dialog box you can add a membrane to the Desmond model system and position the membrane with respect to the solutes.

When you have placed the membrane, a representation of the membrane is displayed in the Workspace. The membrane is represented as two red slabs, with a yellow line perpendicular to the slab planes. The actual membrane molecules are placed when the system builder job is run. This is done by replication of a membrane segment and deletion of molecules whose center of mass lies outside the periodic box boundaries. Molecules that are inside the solute or have significant overlap with it are removed to accommodate the solute.

To open this dialog box, click Set Up Membrane in the Solvation tab of the System Builder panel.

  • Features
  • Additional Resources

Set Up Membrane Dialog Box Features

Membrane model option menu

Select a predefined membrane from this option menu. The available membranes are DPPC, POPC, POPE, and DMPC. The temperature at which the membrane patch was preequilibrated is given in parentheses after the membrane name. Because DPPC has a gel transition temperature around 313  K, the recommended minimum is also 325 K.

Transmembrane atoms ASL text box and buttons

Select the atoms that are inside the membrane, by one of the following methods:

  • Click Select to make the atom selection in the Atom Selection Dialog Box. The ASL expression for these atoms is displayed in the text box when you click OK in this dialog box.
  • Click Set to Helices to select residues whose secondary structure assignment is a helix. This button enters the ASL expression res.sec helix in the ASL text box. If your protein does not have a secondary structure assignment, you can assign it with Edit → Assign → Secondary Structure in the main window.
  • Enter an ASL expression directly into the text box.
Place Automatically button

Place the membrane in the default position and orientation. If you have a protein from the OPM database (http://opm.phar.umich.edu), the membrane is placed using the OPM convention, i.e. the membrane is perpendicular to the z axis with the coordinate origin at the center of the membrane. Otherwise the surface of the membrane is placed perpendicular to the longest axis of the protein. If you select transmembrane atoms, the membrane is placed so that these atoms lie inside the membrane.

If you click this button after adjusting the membrane, the membrane is returned to its default position and orientation.

Place on Prealigned Structure button

Place the membrane according to the current coordinates of the structure in the Workspace. The membrane is placed symmetrically about and parallel to the xy plane, so that the surfaces are perpendicular to the z axis. This means that the protein must be aligned accordingly.

Adjust membrane position option

Select this option to adjust the position of the membrane after it has been placed. You can change the orientation of the membrane using the Workspace rotation (middle mouse) button.

Save Membrane Position button

Save the membrane position to the entries that are selected in the Project Table.

Load Membrane Position button

Load the membrane position from the entry that is selected in the Project Table.

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