Pipeline Pilot users may have built protocols in previous versions with the Clean Molecule component and when they try to run the protocol in the latest version 2023, they will get an error that points to the component location in the previous version. The reason for the error is that the component has been deprecated and it is no longer available under "Components\\Chemistry\\Data Access and Manipulation\\Manipulators\\".

However, it is still available for use under "Components\\Chemistry\\Utilities\\Internals\\Deprecated\\" folder in Pipeline Pilot 2023.

Pipeline Pilot Chemistry product team member also recommends that we can use the Cheshire option in the 2D Coords (Advanced) component, which is a port of the Cheshire Clean Molecule.

A third option is to use the "Clean Structure" component under Materials > Manipulators provided the user has access to this collection.