This is a 3D mode using the Microsoft Direct3D software, which is essentially equivalent to OpenGL. Direct3D is a part of the DirectX drawing software. The main reason for selecting this mode is to display stereoscopically using shutter glasses or a polarizing monitor or projector, if you have a display card which supports stereo only using Direct3D, not OpenGL quad-buffering. See the Stereoscopic Display section in Reference for the requirements and procedures.
This mode also allows anaglyph (Red/Green or Red/Blue) stereoscopic viewing with appropriate software drivers. This requires only cheap plastic colored glasses. The nVidia GeForce graphics cards which support stereo viewing with shutter glasses also support anaglyph viewing - in the nVidia Control Panel, enable Stereoscopic 3D and select "3D Vision Discover" in the Stereoscopic 3D display type option.
Other software vendors such as iZ3D and TriDef supply drivers which may support anaglyph or various other kinds of stereoscopic viewing on your system.
Stereo Viewing with nVidia shutter glasses. The nVidia GeForce display drivers prior to V266 supported stereo viewing only in fullscreen mode, not in a window. If you have an old driver you will have to go into fullscreen mode (Fullscreen button in the Dialog Bar - Left) to see stereo, but you should download the updated driver from nVidia if possible. For smoothest operation of windowed stereo, in the nVidia Control Panel, under Stereoscopic 3D/Set up stereoscopic 3D, in the category "Select when the display is in 3D mode:" choose "Always". If this is set to "Only while 3D programs run", the entire screen may blank out while entering and exiting Direct3D mode and entering and exiting from fullscreen mode. If it is set to "Only while full-screen 3D programs run", there will only be stereo in fullscreen mode, not in the ATOMS graphics window.
In the Direct3D mode, fullscreen, there is no atom identification - the only action of the mouse is to rotate the structure. The shortcut keys have their full effect.
The nVidia settings depth and convergence are not available to the user in ATOMS, because they are controlled by the two ATOMS settings Stereopair Rotation Angle and Perspective Distance. Convergence affects the apparent overall distance of the object - whether it appears to be in front of or behind the screen. However, excessive displacement in either direction can cause difficult in the ability of the eyes to merge the two images (they may become excessively separated on the screen), and also increased prominence of "ghosts" or residual weak images in the wrong eye. Therefore ATOMS always sets the convergence distance equal to the perspective distance so that the center of the structure is essentially in the screen, not in front of or behind it. The stereopair rotation angle then sets the nVidia depth (the term "depth" does not refer to the position of the object front-back, but to the apparent distance between the nearest and the furthest parts of the object).
The nVidia Keyboard Shortcuts or hot keys for changing depth and convergence have no effect in ATOMS, although using the depth keys will bring up a scale showing the relative degree of stereo effect.