Tips for working with Dummy Atoms

Tips for working with dummy atoms

Dummy atoms (*) aren't supported by MoleditPy's built-in 3D pipeline. This page explains why, and how to work around it with the XYZ Editor plugin.

Why dummy atoms don't work directly

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

Recommended workflow

1. Optimize first — perform the standard 2D-to-3D conversion and structural optimization on your target molecule without the dummy atom.
2. Open the plugin — launch the XYZ Editor plugin from the menu.
3. Add the atom — manually add the dummy atom (* or any custom symbol) to the table within the plugin.
4. Adjust position — use the built-in 3D Edit feature to interactively fine-tune the dummy atom's coordinates in the 3D viewer.

Requirements

Requirement	Detail
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	Find and install XYZ Editor from the Plugin Explorer, or browse the moleditpy-plugins wiki. Installation works the same as any other plugin — see Using Plugins

See also

• Using Plugins — installing and managing plugins
• Tips for 2D to 3D conversion
• Tips for 3D editing