5.4 More about the 3D Feature

The fact that a membrane is handled and presented 3-dimensionally establishes room for options.

First of all, you can customize the appearance, activate some helpers and change your point of view.

Another important feature is the detail settings, which do not only take effect on visuals, but play a major role in the precision of geometric calculations.


Moving the camera

The camera in the Membrane View can also be operated by using the mouse.

Here are some controls:

Rotate Hold down the left mouse button while moving the mouse in any direction.
Rotating is only allowed while in Free-Look mode.
Zoom Hold down the middle mouse button and move your mouse up/down to change the zoom level
Translate Holding down the right mouse button while moving the mouse will translate
your camera

The camera is always set to one of 3 possible modes which can be activated in the lower toolbar.

The two buttons on the right will move the camera to a top view on the membrane, either from the extracellular or from the intracellular side. You cannot rotate the camera in these two modes.

To rotate the camera you will have to activate the Free-Look mode (left button).

The coordinate system

The Membrane View shows 2 different helpers concerning the coordinate system which can be toggled on/off in the upper toolbar:

Displays the bars of your coordinate system. The measurement are in anstrom values.

Displays a grid on the X/Z plane of your boundaries. Each mesh measures 10 anstrom in width/height.

Display Mode

The MembraneEditor offers 5 different display modes which can be changed in the upper toolbar. The different atomic display modes are well-known by the usual PDB viewers.


Displays all molecules in their shape mode. This is the most efficient display mode and it is also used by default


Displays all molecules in an atomar representation, while the atoms are rendered in their covalent radii.


Same as 'Covalent', but atoms are shown in their Van-Der-Waals radii


In this mode, all covalent as well as disulfite bonds are displayed.

Balls & Sticks

Same as 'Sticks', but additionally all atoms are rendered in a reduced radius.


Due to the large amount of atoms that have to be rendered in a usual membrane, atomic display modes will slow down the performance significantly! DO NOT use this feature unless your membrane is fairly small, contains only few objects or you own a really fast computer and graphic card.

If you only want to preview your membrane, use the more efficient preview function.

Accessing Settings

All settings regarding the 3D view are located inside menus which can accessed by the 'Open 3D Settings' item either from the toolbar or the program's menubar. It inherits 3 menus, Appearance, Geometric Detail and Controls.

You can use the 'Default' button in order to reset the current menu to default values.

For more information about the settings, read the next page