The molecule search allows users to search by text (name, CAS number) or to draw a molecule. Drawing the molecule can offer more customization possibilities to the search.

To search by drawing the structure of a molecule, a sketcher is available.

Use the different icons representing the atoms / cycles / bonds to draw your molecule.  

A .mol file can also be imported directly into the sketcher:


To save time, instead of importing a file, the name of a structure (IUPAC, common, trade) can also be typed in the "auto-recognize" (import default menu) and the structure will be drawn instantaneously. The auto-recognize feature works with SMILES and CAS number as well. Modifications in order to extend the searched structures can now be drawn in the sketcher.

Differences between a structure with hydrogens drawn out and hydrogens implied in the sub-structure search:

  • In the sub-structure search, if you do not actively draw out a hydrogen on a C, N, O, P, etc., it is considered by the system as a variation point in your sub-structure search. 
  • If you purposely draw the hydrogen on the carbon you lock that position and force the system to search the structure with a hydrogen on that carbon.

You can read the online Help Links for drawing (Marvin JS). For a start: Getting Started with Marvin JS

If you want to go further, you can find here a documentation about the sketcher options, and detailed information about drawing R-groups in Marvin JS.

If you are interested in the query features, which can be drawn in Marvin JS, a summary page is at your disposal.