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Tips for working with Dummy Atoms

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Hiromichi Yokoyama edited this page Aug 4, 2026 · 4 revisions

How to Work with Dummy Atoms (*)

Standard 2D-to-3D conversion (embedding) and 3D structural optimization using RDKit's built-in force fields (like UFF or MMFF) currently do not work with dummy atoms (*). This is because dummy atoms lack the necessary physical parameters required for coordinate generation and energy calculations. However, you can still visualize and process dummy atoms by using the XYZ Editor plugin.

Recommended Workflow

  • Optimize first: Perform the standard 2D-to-3D conversion and structural optimization on your target molecule without the dummy atom.
  • Open the plugin: Launch the XYZ Editor plugin from the menu.
  • Add the atom: Manually add the dummy atom (* or any custom symbol) to the table within the plugin.
  • Adjust position: Use the built-in "3D Edit" feature to interactively fine-tune the coordinates of the dummy atom in the 3D viewer.

Requirements

  • MoleditPy: the XYZ Editor plugin declares PLUGIN_SUPPORTED_MOLEDITPY_VERSION = ">=4.0.0, <5.0.0", so any MoleditPy 4.x release works (the current release is 4.5.1).
  • Plugin Download: You can find and install the XYZ Editor plugin from the MoleditPy Plugins Explorer, or see it listed on Official Plugins. Installation itself works the same way as any other plugin — see Using Plugins.

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