Avogadro for zSpace 1.0 BETA

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Avogadro for zSpace


Status: Version 1.0 BETA

Known issues:

  • zmouse integration is experimental and there are issues with Windows integration (unable to use it for certain windows functions such as selecting files, backgrounds etc. within the application GUI)
  • Large scale models can lag when using high rendering quality (switch to “Force Quick Render” in the zSpace menu)
  • Using labels on molecule models with a large number of labels can cause your stylus rendering to disappear.
  • On a dual display setup, the first run of Avogadro after booting Windows and starting the tracking service for the first time will come up split between both displays.  On the next run of the application, the “Windowed” mode box will be checked.  The workaround is to uncheck the box and launch again or run the application in single display mode (disable laptop display on your demo setup) - This is a known issue with openGL and Unity.
  • Occasionally the application can and will crash. Don't be alarmed, the application is built on an open source project and the original application crashes as well.  Also, this application has not been fully tested, it's a beta test build, considered to be more of a "proof of concept" than anything else.




From the Avogadro web site - “Avogadro is an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible high quality rendering and a powerful plugin architecture.”

This version of Avogadro has zSpace integration for stereo, head tracking, and stylus navigation.  There is also support for using the stylus as a mouse and input support for trackball and space navigator devices.


  • zSpace System Software 2.7 or newer
  • zSpace as primary display (in a multiple display environment) (This is VERY IMPORTANT - failure to launch on primary display will cause issues with stylus and head tracking functionality and alignment)
  • openGL supported video card and drivers


Avogadro Test Build Running Instructions

Before installing and using zSpace Avogadro, we highly recommend that you go to the main web site, download and install the original 2D application and get familiar with using it. In addition to the original application, you will find documentation and FAQs on Avogadro usage.


Main Avogadro Website:

File support:

Avogadro supports many common file types. There are lots of complex protein files (*.PDB) at

Additionally, there are quite a few fragments in *.CML (cellular markup language) within the application that can be loaded.  These are much simpler structures which are easier to visualize and work with for beginners.  These files are located within your installed path, typically C:\Program Files (x86)\zSpace\Avogadro for zSpace\share\avogadro\crystals\{fragment_folder_name}\*.CML


Avogadro for zSpace download link:

Avogadro 1.0 beta download



After downloading, double click Avogadro for zSpace.exe and follow the prompts to install. 


Launching Avogadro for zSpace:

To launch, go to the Windows Start Menu - zSpace - Avogadro for zSpace folder and double click Avogadro for zSpace shortcut to launch.  Optionally you can launch it from the desktop shortcut created during the installation process. 


From the file menu, open a .CML fragment file from your app path C:\Program Files (x86)\zSpace\Avogadro for zSpace\share\avogadro\crystals\.  In there are many folders which contain .CML files you can load.  Once loaded, you should see some sort of molecule structure in the view window.


The following screenshot shows how to control the zSpace settings:



The settings are:

  • Stereo - Enable/disable zSpace stereo
  • Swap Eyes - Manually swap Left/Right eyes (debug tool)
  • Tracking - Enable/disable zSpace head & stylus tracking
  • Force Quick Render - Keep Avogadro in its “quick render” mode for performance
  • Enable zMouse - Enable “zMouse mode” (more below)
  • Trackball - Enable “trackball" mode (more below)
  • Space Navigator - Enable Space Navigator input (more below)
  • World Scale - Adjust the world scale of the scene
  • Change Background - Load an image file as a background image

Note that, outside of trackball mode, the mouse continues to function normally for all features.  In addition, you can use the stylus to guide the mouse like in the Maya plugin – just hold it close to the screen.  There are certain buttons that don’t seem to work with the stylus-driven mouse, such as the red “X” button that closes windows. 

In “trackball” mode (which only makes sense if you have a trackball), the mouse is used to rotate the scene always.  The mouse pointer will disappear from the screen to indicate this.  You can still use the stylus to control the mouse, like in Maya, to access buttons and menus.  Clicking a trackball button will exit the mode so you can get your mouse back.  Additionally, pressing the SPACE bar will enter or exit trackball mode.

The stylus effectively acts as a 3D mouse.  You can draw and move atoms in full 3D.  The stylus vibration function is used at various points to alert you, for example, that you have crossed the threshold above the screen where it switches to driving the Windows mouse instead.

Preliminary support for Space Navigator devices is present.  Click the checkbox in the zSpace tool to enable it.  Currently it only moves the molecule as a whole, similarly to the trackball.  Note that you need to add a line to Settings.xml, in the section Settings/Hardware/Tracker:


                <Target name="Glasses" device_name="IZAtlas" type="HEAD" />

                <Target name="Stylus" device_name="IZAtlas" type="PRIMARY" />

                <Target name="Pointer" device_name="SpaceNavigator" type="SECONDARY" />



The virtual length of the stylus wand is 15cm.  When the zSpace tool is active (press F7 or click the zSpace logo in the toolbar), you can change the length of the wand by pointing at an atom and clicking the right button.  The wand lengthens or shortens as needed to reach the atom, although it will not get shorter than 15cm.

In the zSpace tool, the main button acts similarly to other zSpace demos with stylus:  You can grab the molecule and manipulate it with all 6 degrees of freedom.  If the trackball mode is active, you can spin it at the same time.


Enabling “zMouse mode” (currently very experimental) causes the mouse pointer to be drawn in stereo, so that it has an apparent depth approximately matching whatever it is passing over at any moment.

Avogadro has a “quick render” mode that reduces visual quality during dragging operations, in order to keep the frame rate up.  You’ll notice this when you load a very large molecule.  If the frame rate is really low in stereo, you can use “Force Quick Render” to keep Avogadro in this mode all the time.

One thing you will notice right away is that the default background color (black) is prone to ghosting effects.  This screenshot shows how to change to a more neutral background:


This setting will be remembered next time you start Avogadro. 

Alternatively, you can load a background image using the zSpace Tool’s “Change Background” button.  Certain types of background images are known to reduce the perception of ghosting.  This setting will also be remembered.

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  • Avatar
    Steve Pieper

    The download link on this page doesn't appear to be working...  it takes me to a login screen and then some kind of resume upload site.

  • Avatar
    Eric Tripp

    Hi Steve,

    The link works fine for me. Are you unable to download secure https links?

  • Avatar
    Steve Pieper

    The link is working for me now - thanks!

  • Avatar
    Marek Wróblewski

    It does not work. I've installed. I try to run and nothing happens. zSpace 300 Winsows 10 64 bit. Please help

  • Avatar
    Scott Whitacre

    Avogadro is something we did as a demo. It is not supported, as no demos are. The original developer of Avogadro did not update it to support our newest system software for zSpace 300

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