2D Sketcher Right-click Menus

You can right-click on an atom or bond to access a context menu to perform various actions. If you have a trackpad, you can generally access the context menu by pressing on the trackpad with two fingers, rather than one.

Atom Right-click Menu

 

Right-click with no selection or with the entire structure selected in the drawing area to open a context menu. The options are:

Save Image...
Save image as with File name and Format of either PNG or SVG.
Default is a white background with a 400 x 400 px image.
Select Change ˅ to change to a transparent background and change the image size.
 
Export to File...
Export structure with File name and Format of:
  • MDL SD V3000 (*.sdf *.sd *.mol *.mdl)
  • SMILES (*.smi *.smiles)
  • Extended SMILES (*.cxsmi *.cxsmiles)
  • InChl (*.inchi)
  • PDB (*.pdb *.ent)
  • Maestro (*.mae *.maegz)
 
Flip All Horizontal
Flips entire structure on a horizontal axis.
 
Flip All Vertical
Flips entire structure on a vertical axis.
 
Undo
Reverts previous action.
 
Redo
Reverts undo .
 
Select All
Selects entire structure.
 
Copy All
Copies entire structure to the clipboard.
 
Copy All As
Copies entire structure to the clipboard with the following format options:
  • MKL SD V3000
  • SMILES
  • Extended SMILES
  • SMARTS
  • InChl
  • InChlKey
  • PDB
  • Maestro
 
Paste
Pastes item(s) on the clipboard into the workspace.
 
Clear Sketcher
Clears the workspace.

 

Right-click on an atom in the drawing area to open a context menu. The options are:

+ Charge
Increase the formal charge on the selected atom by one.
 
- Charge
Increase the formal charge on the selected atom by one.
 
Add Unpaired Electron
Increase the number of unpaired electrons on the selected atom by one.
 
Remove Unpaired Electron
Increase the number of unpaired electrons on the selected atom by one.
 
Replace with
Replace selected atom with a Wildcard, Allowed List, New R-Group, or Existing R-group.
 
Edit Atom Properties / Set as Atom
Opens a dialog box where you can set atom properties or add a query to the atom. The dialog will open to the Atom option with the Element field populated with Carbon. Other fields available for input are: 
  • Isotope
  • Charge
  • Unpaired electrons
  • Enhanced stereo

 

 
Edit Atom Properties / Set as Query
When the atom selected is an R-Group, right-click opens to the Query option with the Type field populated with R-Group and the R-Group number set to 1. Other fields available for input are: 
  • Type
    • Allowed List (comma-separated list) | Periodic Table dropdown is shown
    • Not Allowed List (comma-separated list) | Periodic Table dropdown is shown
    • Wildcard (Any heavy atom (A), Heteroatom (Q), Metal (M), Halogen (X), Any or H (AH), Hetero or H (QH), Metal or H (MH), Halogen or H (XH}
    • Specific Element (element) | Periodic Table dropdown is shown
    • R-Group (default set to 1)
  • Number (Only positive numbers may be entered here, from 1 to 99)
  • Isotope field
  • Charge (positive or negative)
  • Unpaired electrons
  • Enhanced stereo (ABS)

 

 
Delete
Delete the selected atom.

 

Bond Right-click Menu

 

Right-click on a bond in the drawing area to open a context menu. The options are:

Flip substiuent

Flip substiuent is not activated by default.

     
Single
Change the selected bond to a single bond.
 
Double
Change the selected bond to a double bond.
 
Triple
Change the selected bond to a triple bond.
 
Up
Change the selected bond to a solid wedge bond.
 
Down
Change the selected bond to a dashed wedge bond.
 
Other Type
Change the selected bond to a Coordinate or Zero-Order, Single Up/Down, or Double Cis/Trans.
 
Query
Add a bond query. The labels added to the bond are: Any, S/D (Single/Double), D/A (Double/Aromatic), S/A (Single/Aromatic)
 
Delete
Delete the selected bond.

 

Atom and Bond Right-click Menu

 

Right-click on a selection that includes both atoms and bonds to open a context menu. The options are:
Invert Selection
If all atoms are selected, clicking this option deselects all atoms. If some atoms are selected, clicking this option deselects these atoms and selects all the other atoms in the molecule.
 
Cut
Cut the current selection.
 
Copy
Copy the current selection.
 
Copy As
Select the format with which to copy the current selection.
 
Modify Atoms
Opens up the Atom Right-click menu. Actions apply to all selected atoms.
 
Modify Bonds
Opens up the Bond Right-click menu. Actions apply to all selected bonds.
 
Replace Selection with
Replace the entire selection with either a New R Group or an Existing R Group.
 
Delete
Delete the selection.