3D Options Tab

images/download/attachments/1805754/Preferences_3D_Options_Tab.png

Name

Description

3D Draw Settings

Stick Diameter

Specifies the width of bonds in stick mode in Angstroms.

Ball Radius

Specifies the size of atom spheres in ball-draw type, measured in Angstroms.

Objects in MarvinSketch

Fog Effect Factor

Sets the fading strength.

No fog: All regions of the structure is displayed with the same line strength and color.

Strong: The fading is at its maximum (molecule is only slightly visible at the far end).

3D Cleaning method

Fine Build

Fine Clean3D builds up conformers of fragments to find low energy conformers. Leaves failed fragments intact.

Fine with Hydrogenize

The build process always adds explicit Hydrogens to the structures which are removed if not present in the original molecule.

This option prevents the removal of extra Hydrogen atoms, otherwise, it gives the same results as Fine Build.

Fast Build

Fast clean, which if fails, performs a fine clean. It accepts any generated structure, and it is the default behavior of the Clean3D function.

Build or Optimize

Builds 3D structure for non-3D molecules and just optimizes the 3D molecules with the Dreiding force field.

Gradient Optimize

Optimizes with the Dreiding force field using the actual structure as starting geometry.