3D Editor

The 3D Editor works in all browsers, including IE11+, Edge, Safari, Opera, Chrome and Firefox, as well as Mobile Safari and Chrome for Android.

The 3D editor controls are modeled from the ChemDoodle® desktop application. Those familiar with the ChemDoodle desktop application will immediately be comfortable interacting with structures in this web-based interface.

The most basic 3D editor input is received from mouse events. In addition to mouse input, there are buttons and keyboard shortcuts that are described in the other tabs.

If you are developer and would like to learn how to install this sketcher, please refer to the EditorCanvas3D documentation.

The buttons presented on top of the sketcher provide functionality as described by the following list. It should also be noted, that in almost all states the following controls are active. Clicking and dragging will rotate the content. Double-clicking will center the content. Scrolling the mouse wheel (or using the pinch gesture) will scale the content. Double-clicking on the background will center the content. Holding the alt key down while clicking and dragging will translate the content.

Undo – Undoes the last performed action.

Redo – Redoes the last undone action.

Zoom In – Increases the rendering scale of the 3D editor.

Zoom Out – Decreases the rendering scale of the 3D editor.

Open File – This button pops up a window that allows a user to paste in the contents of an MDL MOLFile or ChemDoodle JSON to be loaded into the sketcher. This will replace the current content.

Save File – If iChemLabs services are used, then this button will open a file dialog to allow users to save any of the 24 chemical file formats that ChemDoodle supports. Otherwise, this button pops up a window displaying MDL MOLFile content for the selected structure that can be pasted into a text editor and saved with a .mol extension.

MolGrabber – This button pops up a window displaying a MolGrabberCanvas component that can be used to search the ChemExper, ChemSpider and PubChem databases for molecules of interest and then load them into the 3D editor. This feature is only accessible through iChemLabs services. You may want to use the optimize function after you load the molecule into the 3D editor to generate 3D coordinates.

Calculator – Calculates various descriptors for the current molecule. This feature is only accessible through iChemLabs services.

Transform – This is the default state for the 3D editor. Does nothing other than the basic transform behaviors.

Visual Settings – This button pops up a window with controls to customize the graphics rendering of the 3D editor.

Measurements – Using the mouse pointer, hover over the first atom you want to measure the measurement between and it will be highlighted in amber. Click and the atom will be selected and highlighted in blue. Then repeat this for the number of atoms required for the measurement. 2 are required for distances, 3 for angles and 4 for torsions. The order you select atoms is very important. The order should be clearly from one end of the measurement to the other.

Clear – Clears the 3D editor.

Clean – Optimizes the current molecule with 3D coordinates. This feature is only accessible through iChemLabs services.

Group Buttons

At the end of some button groups, there is a small button with a downwards facing arrow. This means that there are more options available for this button set. Just click on this downwards facing arrow and select an option. The button adjacent to the downwards facing arrow will pick up this option and will be automatically selected for use.

Just like in the desktop version of ChemDoodle, the web-based 3D editor implements a copious amount of keyboard shortcuts. All keyboard shortcuts will work regardless of the state or mode the 3D editor is in. But keep in mind that many of these shortcuts also are shortcuts for the browser. So these shortcuts will only work if the mouse is over the 3D editor.

Modifier Shortcuts

Modifier shortcuts are executed by holding down the system meta key, which is ctrl on Windows and Linux and command on Mac OS X.

n Clears the 3D editor.
o Pops up a window to load a chemical file.
s Pops up a window to save the structure in the sketcher in a chemical format.
y Redoes the last undone action.
z Undoes the last performed action.
+ Zooms in.
- Zooms out.
Coming soon!
If the website implementing the web-based sketcher does not access iChemLabs services, then important functionality that you may benefit from is missing from their implementation. Please urge the providers of that service to contact us and provide users like you with premium services.

If you need help for any reason, please view our support options.