In Density Puzzles, Align/Refined buttons will «eat up» one undo step when activated or...

[bertro]

In Density Puzzles, Align/Refined buttons will «eat up» one undo step when activated or when the next tool is used.

[beta_helix]

thanks for reporting this electron Density bug

[infjamc]

Possible short-term workaround:
Conduct a dummy action to create one data point on the undo graph. (Example: wiggle sidechains)

[bertro]

For record, problem is still present in 498.