Structure Cleaning
2D cleaning
2D cleaning of molecules can be performed using the Clean button of the General toolbar. It calculates new 2D coordinates for the atoms on the canvas in order to get the same molecule in an evenly organized fashion.
Partial cleaning of a structure is possible, too. If you have selected fragments of molecules or certain elements of a multimolecular structure, 2D cleaning affects only these selected objects.
The 2D cleaning feature is available only if the server connection is active, and the appropriate web service is available otherwise the Clean button will not appear.
3D cleaning
You can determine the 3D structure of your molecules ("clean them in 3D") by using the Clean 3D on the General toolbar.
The 3D cleaning feature is available only if the server connection is active, and the appropriate web service is available, otherwise the Clean 3D button will not appear on the toolbar.
Structure Validation
Marvin JS only highlights valence errors, but does not correct them, so you should make the necessary corrections manually. In case of recognizing a valence error, Marvin for JavaScript highlights the particular atom with red background.