The Molecular editor tool lets you do a multitude of things very easily. Whether you are working on an experiment or customising your Inventory, once you've finished editing it, your molecule or reaction will automatically be added to your content. Need to work out the stoichiometry or record the hazards of a molecule? No worries, the editor tool does it for you!


Adding a molecule to your content:

In your Experiment/Protocol entry

  1. Type / (slash) in your experiment or protocol entry

  2. Click on 'Data'

  3. Select whether it is 'Input' or 'Output'

  4. Select 'Molecule' in 'Data Type'

  5. Specify the Label

  6. Click on 'Draw molecule / reaction'

  7. Draw a molecule or reaction

  8. Click on 'Done' when finished

  9. Click on 'Done' again once you've specified all necessary fields

Labstep team tip: You can also add a molecule or reaction from the Data tab by following the same procedure.

A GIF showing how to add a molecule to a protocol entry

In other content

  1. Navigate to the content of your choice

  2. Click on 'Add Metadata Field'

  3. Enter a Field Name

  4. Select the Type as 'Molecule'

  5. Click on 'Done'

  6. Click on 'Draw molecule / reaction'

  7. Draw a molecule or reaction

  8. Click on 'Done' when finished

Labstep team tip: You can click on 'Fetch Metadata' and use these information to add as Metadata to, e.g. a resource.

A GIF showing how to add a molecule from a metadata field

Navigating the Tool palette:

Selection tool

  • To select one atom or bond → use the Lasso or Rectangle Selection tool

  • To select multiple objects → use either the Lasso or Rectangle Selection tool

  • To select the entire structure → use the Fragment Selection tool

Labstep team tip: Ctrl+Shift-click with the Lasso or Rectangle Selection tool selects several structures.

A GIF showing how to use the selection tool

Top menu

  • Clear Canvas (1) → clears the drawing area

  • Open...(2) → imports a molecule from a molecular file

  • Save As… (3) → saves it to a supported molecular file format;

  • Undo (4) → reverses a change

  • Redo (5) → reapplies a change that had previously been deleted

  • Cut (6) → deletes an object to make a copy elsewhere

  • Copy (7) → reproduces an object too add in another location

  • Paste (8) → inserts an object copied from elsewhere

  • Zoom In/Out (9) → enlarges or decreases the screen

Labstep team tip: The scaling tool does the same as the zoom in/zoom out one.

A screenshot of the top toolbar

Left-hand side menu

  • Erase (10) → deletes a selected element

  • Bond (11) → adds a bond of your choice

  • Chain (12) → creates a chain

  • Quick shape (13) → adds in a quick shape

  • Charge plus (14) → increases an atom's charge

  • Charge minus (15) → decreases an atom's charge

  • Reaction arrow (16) → enables you to add in reaction elements

  • S-group (17) → draws S-group structures

  • R-group (18) → draws R-group structures

  • Rotate (19) → moves the structure display

A screenshot of the left toolbar

Right-hand side menu

  • H (20) → adds an hydrogen atom

  • C (21) → adds a carbon atom

  • N (22) → adds a nitrogen atom

  • O (23) → adds an oxygen atom

  • S (24) → adds a sodium atom

  • P (25) → adds a phosphorus atom

  • F (26) → adds a fluorine atom

  • Cl (27) → adds a chlorine atom

  • Br (28) → adds a bromine atom

  • I (29) → adds an iodine atom

  • Periodic table (30) → displays the periodic table

  • Reaxys Generics (31) → defines atoms, acyclic and cyclic groups

A screenshot of the right toolbar

Using the drawing tool:

Drawing atoms

  • Adding an atom to an existing molecule → select an atom in the Atoms toolbar, click on an atom in the molecule, and drag the cursor. The atom will be added with a single bond, vacant valences will be filled with the corresponding number of hydrogen atoms.

  • Changing an atom → select an atom in the right-hand side menu and click on the atom to be changed. You can also double click on the atom which will prompt a pop-up enabling you to edit the atom properties. In case of wrong valence, the atom will be underlined in red.

Labstep team tip: The Periodic Table enables you to add an atom from a range of options Single (selection of a single atom), List (choose an atom from the list of selected options), Not List (exclude any atom on your list at that position).

A GIF showing how to draw atoms

Drawing bonds

  • Adding a bond → click the arrow in the right-hand bottom corner of the Bond tool and select a bond type.

  • Changing a stereo bond's direction → click on it to automatically change its direction.

  • Changing a bond type or properties double → click on it and a pop-up will appear.

  • Adding a bond to an atom → click on the atom, the bond will be added at a 120º angle.

  • Adding a bond to an existing molecule → click on an atom in the molecule and drag the cursor, you will be able to choose the degree angle.

  • Drawing consecutive bonds → use the Chain tool, you can change the atom type

Labstep team tip: Clicking with the Single Bond tool switches the bond type cyclically, from Single to Double, to Triple, to Single again (and so on).

A GIF showing how to draw bonds

Using templates

  • Adding a ring to the molecule → select a ring from the toolbar and click inside the drawing area, or click on an atom/bond in a molecule.

  • Selecting a template + clicking on an atom in an existing structure → adds the template to the structure connected with a single bond.

  • Selecting a template + dragging from an atom in an existing structure → adds the template directly to this atom resulting in a fused structure.

  • Dragging an atom in an existing structure → results in a single bond attachment if dragged more than ½ of the bond length. Otherwise a fused structure is drawn.

  • Selecting a template + clicking on a bond in an existing structure → creates a bond-to-bond fused structure. The bond in the initial structure is replaced with the bond in the template. This procedure doesn’t change the length of the bond in the initial structure.

  • Dragging the cursor relative to an initial bond → applies the template at the corresponding side of the bond. The added template will be fused with the default attachment atom or bond preset in the program.

A GIF showing how to use templates

Stoichiometry & Molecule metadata:

Using the stoichiometry table

The Stoichiometry Table enables you to obtain quickly and easily information about a molecule. Simply draw a molecule, click on the refresh icon in the table's right-hand corner and that's it!

A GIF showing how to use the stoichiometry table

Fetching a molecule's metadata

You can draw a molecule and quickly obtain its metadata. If you draw more molecules just click on the refresh icon next to 'Molecule Metadata' and Labstep will fetch their metadata!

A GIF showing how to draw a molecule

Using Files:

The Molecular editor supports MDL Molfile and RXN file, which can be entered either manually or from files.

'Open...' button → imports a molecule from a molecular file.

A GIF showing how to open a molecular file

Save As… buttons → saves a molecule as a supported molecular file format of your choice. Choose from MDL/Symyx Molfile or Daylight SMILES, then simply copy paste it.

A GIF showing how to save a molecular file


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