Pipette Sketcher - Overview

Last Updated: Jan 25, 2016 09:53AM PST

Summary: Pipette Sketcher allows easy sketching of chemical structures and reactions. The detailed features are described below.

Covered Topics

Clicking a link will scroll the page to the relevant section.

Getting Started with Pipette Sketcher

Tip: You can try out Pipette Sketcher on our demo servers in the cloud:

Note that these servers are not set up for production use and you should not submit any data that is proprietary.

Pipette Sketcher has many advantages over the range of other chemistry sketchers available. Noteworthy features of Pipette Sketcher include:

  • Works in modern web browsers, Microsoft Windows touch devices, and Apple iPad and iPhone.
  • Provides automatic layouts of compounds as they are drawn, including layout to pre-defined templates.
  • Displays context-sensitive changes based on the selected atom, bond, or structure.
  • Supports lists of compounds.

Pipette Sketcher Workspace

When the sketcher is first opened, two main areas are displayed:

  • Drawing area (left) Where your structure is rendered. Includes icons to clear the drawing area and undo or redo changes.
  • Toolbox (right) Shows context-sensitive changes you can apply to the current structure. Options for starting the structure are initially displayed.


Drawing Area Icons

Icon Description
clear.png Clears the drawing area.
 undo.png Undo last update.
redo.png Redo last update.


Drawing Your First Compound

  1. In the following example, you can draw vinyl benzoate as your example structure.
  2. Select the benzene starting structure.
  3. Select one of the atoms to see the available changes.
  4. Select the carboxylic acid change. Note the selected atom changes as the sketcher predicts where we are likely to modify next.
  5. Select the ethyl change.
  6. Select the final bond in the chain to see the available bond changes.
  7. Finish by selecting the double bond.

Working with Multiple Components

The previous example (Drawing Your First Compound) shows how selection of atoms and bonds affects the tools shown in the toolbox. There is a third type that allows selection of a structure.

Through selection of a structure, additional components can be added, as shown in the following illustrations:




Note: Individual structures can also be rotated, flipped or reordered as desired.

Importing .mol Files

  1. To import a .mol (or.rxn) file, drag and drop the file into the drawing area.
  2. Then use it as your starting structure.

Copying and Pasting

Use the following shortcut keys to copy, paste, and cut:

Action Keyboard Shortcut
Copy CTRL + C
Paste CTRL + V
Cut CTRL + X

To select a structure:

  1. Click next to the structure to display the blue box.
  2. In the sketching tool that you want to paste the structure into, press CTRL+C (copy) and CTRL+V (paste).

Support for Third-Party Applications 

Chemistry sketchers that can read and write .mol  and .rxn files from the clipboard can exchange structure with the Pipette Sketcher. The following applications are supported:

  • BIOVIA Draw: v4.2: Supports copy/paste. Note that to copy a structure to the clipboard you need to use 'Edit/Copy As/Molfile' or 'CTRL + M'.
  • ChemDraw v13: Supports copying as SMILES and pasting into Pipette Sketcher.
  • ChemDraw v14:  Supports copying in ChemDraw and pasting into Pipette Sketcher. The file is transferred as a molfile object.

Keyboard Shortcuts

Many changes have keyboard shortcuts available.

  • To access a shortcut, hover over the keyboard icon at the bottom of the toolbox:

The keyboard shortcuts are overlaid on the changes and look something like this:


Lists of Compounds

If you send a list of compounds to the sketcher, (for example, from Pipette Analysis), additional icons are displayed in the drawing area.

Icon Description
Add.png Page through the list for items to add.
Remove.png Page through the list for items to delete.

Use these icons to page through the list for items that you want to add and remove from the list, and for persisting any changes to the structure.


Detailed Changes

Some of the board groups of changes are listed below.


Change Examples Notes
Sprout a ring ppt_sprout_ring.png

Adjacent bonds can be multi-selected to allow ring sprouting from several bonds.

See Attaching Rings with Pipette Sketcher.

Change bond type ppt_change_bond_type.png  
Remove bond ppt_remove_bond.png
  • If bond removal results in two separate compounds being formed, only the largest one is kept.
  • To keep both compounds, ensure there is an empty fragment before you break the bond.
Add/remove atom from bond ppt_add_remove_atom_from_bond.png



Provides an easy way to expand and contract rings and chains.
Switch to haptic ppt_switch_to_haptic.png

Allows drawing of compounds such as ferrocene.


See Creating Haptic Bonds with Pipette Sketcher.


Change Examples Notes
Attach group ppt_attach_group.png  
Connect two atoms ppt_connect_two_atoms.png  
Remove atom ppt_remove_atom.png


Change atom type ppt_change_atom_type.png You can select from the default atom list or from the periodic table. If you frequently use particular atoms from the periodic table, they will make their way onto the default list of atoms.
Modify charge ppt_modify_charge.png  
Modify isotope ppt_modify_isotope.png The two most common isotopes are shown by default, but once you select one of these, you can increase and decrease the mass number as needed.
Atom list ppt_atom_list.png  


When launched in reaction mode, the sketcher behaves the same as it would with multiple components, but groups the components into reagents and products. To launch the sketcher in reaction mode append "?chemistry=reaction" to the URL, e.g. https://sketch.sciencecloud-services.com/pipettesketcher/?chemistry=reaction


Selecting Multiple Atoms and Bonds

You can select multiple atoms or bonds by doing the following (depending on device):

Device Description
Non-touch Hold the CTRL key when clicking on the bonds.
Touch Tap the atoms or bonds together or in quick succession.

Note: By selecting multiple adjacent bonds, rings can be added to several bonds. See Attaching Rings in Pipette Sketcher.

Layout Templates

The layout of structures is performed by Pipeline Pilot using any structure templates defined in the Chemistry collection. You can add new templates for your scaffolds, if they are not displayed to your liking.

Tip: For further details on how to add more templates, see the component reference help in Pipeline Pilot for the 2D Coords component.

Note: The Pipette Analysis and Pipette Sketcher API dynamically download code from a cloud server to provide automatic updates. This eliminates the need to manually download and install the software, saving you time. You can control which updates to install through the Admin page for Pipette in the Admin Portal.


Pipette Sketcher Features and Structure Examples

Pipette Sketcher and Stereochemistry

Creating Haptic Bonds with Pipette Sketcher

Attaching Rings with Pipette Sketcher

Creating Markush Structures with Pipette Sketcher

seconds ago
a minute ago
minutes ago
an hour ago
hours ago
a day ago
days ago
Invalid characters found