Stereoscopic Display Modes
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Improved technology has made stereoscopic viewing, that is viewing still images and movies with separate left- and right-eye images to give apparent depth, better quality and and more common on computers and televisions. As far as ATOMS is concerned, there are two separate kinds of stereo-enabled video cards of the most recent types. At present, most software stereoscopic drivers for these cards appear to be available only for Windows.

The 3D Quad Stereo Drawing Mode is available only for graphics cards supporting OpenGL quad-buffered stereo. It is potentially supported for Macintosh and Linux as well as Windows, though driver software does not seem to be available yet for them. The Quadro series of cards from nVidia actually supports either Direct3D or quad-buffered OpenGL stereo.

Direct3D stereo in Windows (only) is supported by the nVidia GeForce series of graphics cards,with their 3D Vision package, and perhaps some others. The GeForce series only supports stereo using Direct3D i(not any kind of OpenGL).

With either type of video card there are basically two types of viewing hardware.

1) Shutter glasses. The images are drawn independently and flashed alternately on the screen at a high rate - 120 times per second in the latest computer implementations, for example those supported by both the nVidia Quadro and GeForce series of display cards. A 120 Hz monitor is required, and it must be viewed with special shutter glasses which blank out the left and right eyes alternately in synch with the images on the screen. Projectors and projection TVs are also available.

2) Polarizing monitors or projectors. The monitor or projector simultaneously or alternately (very rapidly) generates two images which are viewed with glasses with the two lenses polarized at 90 degrees to each other, or with different circular polarizations. Movie theater 3D (stereo) systems use a more elaborate variant of this method. It does not require expensive shutter glasses, only relatively inexpensive polarizing glasses for each viewer.

These types of hardware stereo viewing are full-color and should not be confused with the old two-color (red-green) anaglyph technology which really only shows monochrome or bi-chrome images. ATOMS has always supported stereo viewing using two spatially separated images combined with the naked eye or an optical viewer - this type of technology goes back to the 19th century.

The terminology for stereo viewing can be somewhat confusing. In movie theaters and television, the term 3D means stereoscopic viewing, that is separate images for left and right eyes. In computer and video-game graphics, the term 3D has been applied to several kinds of software techniques, at present primarily OpenGL and Direct3D, which keep track, pixel-by-pixel, of the third dimension in drawings and thus typically produce more realistic images than 2D line and space-fill drawings, though they are not necessarily stereoscopic (no separate images for left and right eyes). This is the way the term 3D is used in all ATOMS literature. OpenGL and Direct3D may be used in ATOMS for single non-stereo images as well as stereo (2D images may also be shown as stereopairs with ATOMS, although this is usually inferior to using a 3D method).

ATOMS in the past has used only OpenGL, which is available for Windows, Macintosh and Linux. ATOMS now supports stereo viewing using the quad-buffered OpenGL method, which is currently available on the Quadro series of video cards from nVidia and some other video cards.

A Direct3D drawing mode has been added to ATOMS for Windows to support stereo viewing with GeForce cards and any others which require Direct3D. This is selected in the Display menu, or with the Drawing Mode drop-down the Dialog Bar - Left.

Older Shutter-Glasses Systems

Older stereo display drivers from nVidia, which worked only on Cathode-Ray-Tube monitors, - not flat-screen LCD monitors, supported Direct3D and OpenGL without quad-buffering. This system works with inexpensive shutter glasses, but if the refresh rate of the monitor is less than 100 Hz or so the flicker tends to be excessive. Such systems are basically outmoded and may not be supported by manufacturers.

Changes in operation of ATOMS

In order to keep the total number of options to a minimum, what were formerly Display Modes have now been separated into Model Modes and Drawing Modes. The Model Mode specifies the type of model which represents the structure, and includes Standard, Ellipsoid, Cavities and Protein. The Drawing Mode specifies which computer technique and viewing mode is used, and includes 2D single, 2D stereopair, OpenGL single, OpenGL stereopair, OpenGL quad stereo and Direct3D. The 2D modes use essentially line and fill drawing, which is suitable for schematic drawings for publication, for example, though shading is available in ATOMS. The 3D modes - OpenGL and Direct3D - use generally more realistic lighting and superior interpenetration relations, and usually look better on screen or in full-color high-resolution printed images. The OpenGL 3D system software is available on Windows, Macintosh and Linux, but Direct3D is available only on windows.

An additional 3D mode, Direct3D, which is available only on Windows, has been added. This is the Drawing Mode which is required for stereo viewing with nVidia GeForce display cards or any others which support Direct3D only. It may be either full-screen or windowed, with the latest nVidia drivers.

Selection of Stereo Viewing Methods


Simple stereopair methods. These allow stereo viewing using no aids or inexpensive glasses or optical viewers. The stereopair modes allow stereo viewing with or without optical aids, but these modes have limitations; the stereopair modes halve the size of the image and the other image is always visible, giving three images (unless some special type of viewer is used).

Hardware stereo methods. In these methods a single image drawn by ATOMS is split into left- and right-eye images by the display hardware, or actually its resident software. Then the two images are displayed on screen, either alternating rapidly in synchrony with shutter glass, or as two differently polarized images. Any of several ATOMS Drawing Modes may need to be used, depending on your video card and monitor.

1) Cards or driver software which support OpenGL quad-buffering, such as the nVidia Quadro series: Select the 3D quad stereo option in the Drawing Mode drop-down box in the Dialog Bar - Left or in the Display menu. Stereo can be shown either in a window or full-screen. The program itself sends the two completed images or objects to two separate buffers, so both the perspective distance and the stereo rotation angle ( = depth or stereo separation) are controlled by ATOMS; perspective distance is changed onscreen with the SHIFT-P and SHIFT-[ keys and the rotation angle with the SHIFT-A and SHIFT-S keys.

Setting up nVidia 3D Vision for quad-buffered OpenGL. In the nVidia control panel, select Manage 3D Settings in 3D Settings. In the Global Settings tabe, the Global presets option should be set to "3D OpenGL Stereo". It may then be necessary to select the particular setting Stereo - Display Mode and set it to "Generic active stereo (with NVIDIA 3D Vision)".

2) nVidia GeForce cards which support their 3D Vision system, and any other display cards which support only Microsoft Direct3D (DirectX). Click on the Direct3D button in the Dialog Bar - Left or the Direct3D option in the Display menu. These cards will also display in anaglyph (red-green glasses) mode without shutter glasses or a special monitor. In this stereo mode, or any other except quad-buffered OpenGL, the program sends only a single drawing (or really, a 3D object) to the video card, which then rotates the image one way for the left-eye image and the other way for the right-eye image.

For full-color operation these options will also require either the nVidia 3D Vision shutter-glass kit and a compatible 120 Hz monitor or a compatible projector, or a stereo polarizing monitor and polarizing glasses. Other hardware and software driver combinations may also be available.

3) Older nVidia cards or some other card with stereo driver software, a CRT monitor and shutter glasses. These may work with the Direct3D option as in 1) and/or with the 3D single option in the Drawing Mode drop-down box in the Dialog Bar - Left or the Display menu. This will only work in full-screen. Like Direct3D in 1) above, ATOMS sets the perspective distance but the stereo rotation is controlled by the video driver.

Shortcut keys for controlling ATOMS images. Since stereo images may require full-screen viewing in which menus are not available, the keyboard shortcuts for modifying or animating the images have been revised and extended.

Additional Details

In ATOMS the perception of depth in stereoscopic viewing is affected by two parameters, the Stereopair Rotation Angle, and the Perspective Distance; both are set in dialogs in the Input2 Menu, or in the DialogBar - Right. A value of about 100 Angstroms for perspective distance and about 1-3 degrees for rotation angle are good starting points.

In viewing real life objects setting the perspective distance would fix the stereopair rotation angle because the human eyes are a fixed distance apart. However in viewing objects on an Angstrom scale the interocular distance is arbitrary, and thus it is possible to set both parameters - in effect the stereopair rotation angle fixes the interocular distance or the scale of the atomic structure relative to the viewer.

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 in the plane of the screen, not in front of or behind it. The stereopair rotation angle then fixes the nVidia depth parameter, which is really the interocular distance (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.

The control of depth and convergence by the ATOMS parameters applies only to the nVidia 3D Vision system. If other video cards or software drivers are used, the controls supplied may have different names; depth, separation and/or convergence and the action of each may involve both translation of the image on screen and rotation. Considerable adjustment of these controls may be required to get the desired stereo effect and an acceptable level of comfort. In particular, it is usually best to adjust the two images without wearing any glasses so that their physical separation is least at the center of the object. In nVidia 3D vision, this would be done by adjusting convergence (but is actually done automatically by ATOMS).

If the perspective distance is small in ATOMS, the projection of spherical atoms will be elliptical on the screen, and while this may actually be what the eye would see at a short distance, such a projected image is usually unsatisfactory in practice. Thus the perspective distance should usually not be decreased beyond the point at which atoms begin to look non-spherical.

There is no stereo rotation or stereo effect at all in Direct3D if the projection is orthographic rather than perspective - that is if Perspective is not selected in the Input 2 menu. Therefore, ATOMS always uses perspective projection in the Direct3D mode, with the perspective distance entered in the Perspective dialog (Input2 menu). If that distance is zero, a plausible value is entered based on the dimensions of the structure.

In real life when attention is directed to a near object, not only is each eye directed towards that object, but the focus is adjusted; viewing a near object causes distant objects to go out of focus or become blurred and vice versa. This enhances perception of depth. On a computer or movie screen the focus cannot be changed, and this may interfere with depth perception for some people. Of course everything drawn by ATOMS is always in focus, unlike a non-animated movie which is recorded by cameras which change focus like the eye. In ATOMS, you may select fog, which only fades out the colors from front to back and does not change the focus.