6.5 3D-Settings

This page describes all options concerning the 3d-mode. Those can be acessed by 'Open 3D Settings' .

Appearance

Brightness Ambient Light

Changes the overall brightness of all visible objects in the view.

A high and a low ambient light setting

Directional Lights

Toggles the 2 additional light sources on or off

Left: All light sources on.    Right: All light sources off

Shininess Proteins / Lipids

Sets the intensity of light reflection on molecule surfaces. The settings for proteins and lipids are done seperately

A high and a low shininess

Polygon Mode

You can choose between the 2 possible modes for rendering the objects:

With a closed surface (Filled) or

in their transparent triangle mesh (Wireframe)

The filled polygon mode

If you display the objects in mesh-mode, you are able
to see through them

Geometric Detail

In this menu you can set up parameters used when a 3D object gets created.

NOTE: These settings do not only affect the rendering performance. They also play a major role at collision detection. That means that higher settings increase the correctness and minimize overlaps between molecules while a lower setting speeds up the collision detection significantly.

In order to apply any changes for already constructed objects, use the 'Refresh Geometry' button located in the toolbar.

Shape Collision and Construction

First of all you can choose to activate the Shape Collision. Using this option, the molecules will be completely surrounded by shapes. Although if you have a lipid with free space between its tails, this space will be connected. So overlapping of different lipids is deactivated. Deactivating this option, the Collision Detection will work faster.

Then you will have to choose between automatic or custom detail settings. Automatic detail ensures that really all atoms get involved in the construction of the shape. Custom detail does not guarantee that, but it may lead to a better performance, especially when the molecules get parsed for the first time.

If custom detail is selected, you will be able to access the following 3 sliders:

Precision Modifier

The dependency between the size of a molecule and the number of levels used while constructing its 3d object in vertical order. The value you  enter represents the number of Levels x (height/100)

Min. Precision

Ensures that all molecules have at least a minimum detail, e.g. when one is very small

Number of Vertices

The number of vertices that are taken into account for an object. The higher the value, the more vertices per level will be used

The objects at lowest detail settings possible

The objects when higher detail settings are used

Atom Collision

This section allow you to choose wether you want to respect the atom radiuses during collision detection, too. If you enable this feature you will be able to define an additional minimal distance between the atoms of two molecules. This may be interresting if you prefer uncongested membranes where atoms are not too close to each other, like some molecular dynamic tools do.

NOTE: It is possible to deactivate Shape and Atom Collision. This maybe interesting, if you want to shift different Molecules very close to each other. But using Membrane Algorithms, some of them will not work at all and/or will not terminate. So keep in mind to activate the collision detection again.

Controls

Mouse Sensitivity

Sets the mouse sensitivity for looking around in the 3D view

Dragging of Proteins

En- or disables the capabiltity to move proteins while using the Free-Look mode. Disabling will avoid annoying unintended displacements