Labguru now integrates Ketcher, a powerful chemical drawing tool, to enhance your experience in working with chemical structures. With Ketcher, you can easily draw, edit, and manage chemical structures directly within Labguru’s platform. The tool can be used to design chemicals, draw reactions, and manage structures.
Opening Ketcher in Labguru
You can launch Ketcher within Labguru in several ways:
Chemical Structure Search: Navigate to the Compound collection index page and click on the magnifying glass icon to open the Ketcher editor. For more information click here.
Registering New Molecules: Click on 'New Compound' on the Compound collection index page. The Ketcher will be integrated into the form to describe the structure of the compound. For more information click here.
ELN Entries: While working in the ELN, use the Ketcher editor as part of the Compound or Reaction element. Click here for more information.
Ketcher Canvas Overview
On the Ketcher canvas chemical structures may be drawn or modified. A full-screen option is available for easy navigation and editing.
The toolbar around the canvas allows easy access to drawing and editing tools.
Selecting Structures
Selection Tool: Use this to highlight and work with individual atoms, bonds, or entire structures. You can also use rectangle selection or freehand selection (lasso).
Shortcuts:
Ctrl-A: Select all structures on the canvas.Ctrl-click: Select an entire fragment.Shift: Select multiple fragments while maintaining the current selection.
Transforming Structures
Move: Drag selected structures to reposition them.
Rotate/Flip: Use the rotate tool to rotate structures or flip them vertically/horizontally.
Drawing Rings, Atoms, and Bonds
Rings: Select from a variety of ring templates located at the bottom of the canvas. Clicking on open space will insert the ring, or you can attach it to an existing structure.
Structure library: A wide variety of templates and functional groups are available to add to the canvas from the SL menu at the bottom of the canvas.
Atoms: Add atoms by selecting them from the right-hand toolbar. To see all available atoms open the Periodic Table (PT).
Bonds: Use the bond tool to add, modify, or delete bonds. Click on an atom and drag to create a bond. Clicking repeatedly on the same bond cycles through single, double, and triple bonds.
Charge: Select the Charge Plus or Charge Minus tool and click consecutively on an atom to increase/decrease its charge.
Marking S-Groups
In order to describe repeating fragments in a molecule, use the S-group tool and define a Multiple group.
Using Stereochemistry
Ketcher supports enhanced stereochemistry, allowing you to represent molecules with up/down wedges and to determine R/S and E/Z configurations.
Drawing Reactions
Chemical reactions can also be created and edited with Ketcher.
Draw Reagents and Products: Start by drawing the reagents and products using the same tools and methods described for drawing individual chemical structures.
Add Reaction Arrows: Use the Reaction Arrow Tool to insert an arrow between reagents and products. A variety of arrow types are available to suit your reaction needs.
Insert Plus Signs: To indicate multiple reactants or products, use the Reaction Plus Tool to add plus signs (
+) between molecules in your reaction equation.Map Atoms Between Reagents and Products: Use the Reaction Mapping Tools to map corresponding atoms between reagents and products, which helps visualize atom tracking in the reaction process. The available tools include:
Reaction Auto-Mapping Tool: Automatically maps atoms based on the structure.
Reaction Mapping Tool: Manually map atoms between reagents and products.
Reaction Unmapping Tool: Remove any existing mappings if needed.
Saving and Exporting
Ketcher provides the ability to load and save structures and reactions in:
DL Molfile (v2000 and v3000)
RXN file format
InChI String
ChemAxon Extended SMILES
ChemAxon Extended CML file formats
For more information on Ketcher please click here.