How to generate a 3D conformer from a 2D molecule using the user interface (June 2, 2025)

Estimated read time: 2 minutes.

Question: I want to generate a single conformer from my 2D input molecule. How can I do this through the user interface instead of using the floes?

Answer: Molecules added to Orion via the user interface sketcher are typically in 2D and lack 3D coordinates. While conformer generation can be performed using floes, for individual molecules it is often more efficient to generate a 3D conformer directly from the 3D & Analyze page.

Here’s how:

Step 1: On the 3D & Analyze page, expand the molecule record. You’ll notice a red 0D or 2D label, indicating the absence of 3D coordinates. Click the arrow to show more (Step 1a), then select Generate Coordinates (Step 1b).

Step 2: Once the 3D coordinates are generated, the molecule will automatically be repositioned in the viewer. To recenter it, simply click the arrow again (Step 2a) and select the Fit button to center and zoom the molecule displayed on the screen (Step 2b).

To learn more, visit the 3D & Analyze page documentation to learn more about 3D editing in Orion.