Avogadro version:1.100.0
Operating system and version:
MacOS 15.3
Expected Behavior
Open .out files from Gaussian calculation to view and manipulate model, and animate normal modes.
Actual Behavior
Molecular model from Gaussian .out files will “disappear” (the model seems to fade into the background with a largely opaque black foreground) upon manipulation (e.g. rotate, translate, animate normal mode). Can click away to another molecule and click back and the model is now visible. However, again trying to manipulate model causes it to disappear. Also, with the Gaussian .out molecule active, clicking on any other molecule will also cause that model to disappear. The second model will reappear after clicking in the main window and behave normally in terms of visibility.
Not quite sure what’s happening, but two possibilities:
Go to View → Rendering… and turn off fog and ambient occlusion (shadows)
Other possibility is that the ball-and-stick opacity is changing somehow. If you click on the … next to Ball and Stick in the display types, you can check the settings
Indeed unchecking the fog option in View-> Rendering made the model visible and it stayed that way.
Also, notching the opacity slider to just less than the max (with fog enabled) sort of worked in that the problematic .out model was visible but when I clicked on another molecule, it was not visible (fog I guess).
It is odd that this is triggered by the Gaussian file.
Thanks for your time.
We’re still tuning the fog effect. It’s based on distance to the camera, so it’s more a question of the particular frame-of-reference for that molecule than any particular file.
Thanks for the report though, I’ll make sure we check that file in tuning the effect.
