Atomic Blender PDB/XYZ

Blender · Blendphys

Atomic Blender PDB/XYZ is a free Blender add‑on that imports atomic structures from PDB and XYZ files, representing each atom as a ball and optionally showing sticks when defined in PDB files.

Workflow1.9.1

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Developed by Blendphys.

Atomic Blender PDB/XYZ preview
Atomic Blender PDB/XYZ · Blendphys

About Atomic Blender PDB/XYZ

Atomic Blender PDB/XYZ imports atomic structures such as molecules, crystals, clusters, particles and surfaces described in PDB (.pdb) and XYZ (.xyz) files. The add‑on reads all atom coordinates and creates a ball for each atom in the Blender scene; sticks are displayed only when explicitly listed in a PDB file. Structures are built using Blender’s vertex‑instancing method, allowing fast loading and responsive handling of models with 1,000 atoms or more. The importer is accessed via File → Import → PDB (.pdb) or File → Import → XYZ (.xyz). Developed by Blendphys (Clemens Barth), it is compatible with Blender 4.2 LTS and newer and is released under the GNU GPL v3.0 or later. Version 1.9.1 (May 2024) includes bug fixes for stick handling and camera/light loading.

Features

  • Imports atomic structures — molecules, crystals, clusters, particles and surfaces — from PDB (.pdb) and XYZ (.xyz) files
  • Reads the coordinates of all atoms and represents them as balls in the Blender world
  • Shows sticks when they are explicitly listed in a PDB file (sticks are PDB only)
  • Builds structures with Blender’s instancing vertices method for fast loading and handling in the 3D View
  • Handles atomic structures with 1000 atoms and much more
  • Accessible from File → Import → PDB (.pdb) and File → Import → XYZ (.xyz)

Best for

Blender users who need to bring PDB or XYZ atomic coordinate data into Blender as 3D geometry.

Frequently asked questions

Does Atomic Blender PDB/XYZ work with Blender 4.2?

Yes. The add‑on is compatible with Blender 4.2 LTS and any later Blender release.

Can Atomic Blender PDB/XYZ import both PDB and XYZ files?

Yes. It can import both PDB (.pdb) and XYZ (.xyz) files, creating balls for each atom; sticks are only read from PDB files.

Does Atomic Blender PDB/XYZ show bonds between atoms?

Sticks (bonds) are displayed only when they are explicitly defined in a PDB file; XYZ files do not include bond information.

Can Atomic Blender PDB/XYZ handle large atomic structures?

The add‑on uses vertex instancing, allowing it to handle structures with 1,000 atoms and more while keeping the viewport responsive.

Is Atomic Blender PDB/XYZ free to use?

The add‑on is free and released under the GNU GPL v3.0 or later.

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