Marvin allows you to clean your molecule in either 2D or 3D.

Cleaning in 3D can lead stereoinformation loss (i.e. atropisomerism) or creation ( i.e. chirality not defined in 2D).

Cleaning will calculate new coordinates for the atoms. Generating conformers and choosing the favored one is also supported. For more information on molecule cleaning, please visit this link.

You can initiate cleaning via the Structure > Clean2D/3D submenu or using Ctrl+2/Ctrl+3 shortkeys.

  • Clean 2D

    • Clean in 2D images/download/attachments/48075576/clean2D24.png (shortcut :Ctrl+2) cleans the molecule(s) in 2D

    • Clean and Arrange in 2D images/ (shortcut :Ctrl+Shift+2): cleans the molecules and places them in the center of the canvas

    • Hydrogenize Chiral Center: adds an explicit hydrogen with a wedge bond to chiral centers which have no terminal atoms as substituents

    • Clean Wedge Bonds: changes wedge bonds for convention display

      Clean in 2D works as Clean and Arrange in 2D if the structure contains: amino acid, coordinate bond or position variation bond.

  • Clean 3D

    • Clean in 3D images/download/attachments/48075576/clean3D24.png : cleans the molecule(s) in 3D

    • Cleaning Method: choosing from various methods

    • Display Stored Conformers: works only if conformers of the sketched molecule had been generated with the help of the Conformer plugin, choosing the "Store conformer information in property field" option. See details in the plugin's documentation .