Is there a way for me to save a customized appearance (e.g., atom colors, etc.) of a molecule so that those settings can be re-applied or automatically applied when I re-open the project file?

Changes to the appearance are persistent: if you change the color, atom or bond style, atoms displayed, or materials, this information is saved in the project for the entries that you change.

If you want to store a particular style, you can use the Workspace Style Settings to set up the appearance as you want it, and then apply these settings to the Workspace whenever you want. However, there is no facility for creating a named style and applying it whenever you want.

You can also create custom color schemes that you can apply whenever you want - see the Customizing Maestro chapter in the Maestro User Manual.

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