by Blendphys·Workflow
Images © Blendphys. Used for product review; image policy.
Earns its place in the Blender extensions library for turning PDB and XYZ coordinate files into 3D geometry, using vertex instancing to keep large structures responsive in the 3D View.
Atomic Blender PDB/XYZ imports atomic structures such as molecules, crystals, clusters, particles and surfaces that are described in PDB (.pdb) and XYZ (.xyz) files. The add-on reads the coordinates of all atoms in the file and represents each atom as a ball in the Blender scene. Sticks are described in PDB files only and are shown when they are explicitly listed in the PDB file.
Structures are built using Blender's instancing vertices method, which keeps loading and general handling inside the 3D View fast. Atomic structures with 1000 atoms and much more can be handled. The importer is reached through File → Import → PDB (.pdb) and File → Import → XYZ (.xyz).
Built by Blendphys (author Clemens Barth), the add-on is compatible with Blender 4.2 LTS and newer and is released under the GNU General Public License v3.0 or later. Version 1.9.1 brought small bug fixes, including changes to stick handling and camera and light loading.
Atomic Blender PDB/XYZ is best for blender users importing atomic structures from PDB and XYZ files and representing atoms as 3D geometry.
Atomic Blender PDB/XYZ is completely free to download and use.
Atomic Blender PDB/XYZ is compatible with Blender 4.2 LTS and newer, so it runs in Blender 4.2 and later releases. Version 1.9.1 was published in May 2024. You can add it by dragging and dropping the add-on into Blender, or by downloading it and using Install from Disk. Once installed, the importer appears under File → Import → PDB (.pdb) and File → Import → XYZ (.xyz), where you point it at your coordinate files. If you run an older Blender release, the listed compatibility begins at 4.2 LTS.
Atomic Blender PDB/XYZ imports atomic structures described in both PDB (.pdb) and XYZ (.xyz) files. It reads the coordinates of all atoms in the file and represents each one as a ball in the Blender world. These structures can include molecules, crystals, clusters, particles and surfaces. The importer is available from the File → Import menu for each format, so you can bring in PDB or XYZ data depending on which file you have. Sticks between atoms are read from PDB files only, while XYZ import covers atom coordinates.
Atomic Blender PDB/XYZ shows sticks, but they are described in PDB files only and appear when they are explicitly listed in the PDB file. XYZ files describe atom coordinates without sticks, so bonds are not drawn from XYZ import. Version 1.9.1 included several stick-related fixes: it removed a few pitfalls when creating sticks and gave joined sticks a better name. That release also removed the 'number of sticks to be joined' option, which never worked correctly. If you need bonds shown, use a PDB file that lists them.
Atomic Blender PDB/XYZ uses Blender's instancing vertices method to build atomic structures, which keeps loading and general handling inside the Blender 3D View fast. Atomic structures with 1000 atoms and much more can be easily handled with this approach. Because the atoms are built with this Blender-specific method, the viewport stays responsive as structures grow. This makes the add-on suited to molecules, crystals, clusters, particles and surfaces that contain large numbers of atoms. For more detail on the method, the developer points to the add-on's wiki page.
Atomic Blender PDB/XYZ is listed as free here and is released under the GNU General Public License v3.0 or later. For the current licensing terms and any details, check the developer's page. The add-on can be added by dragging and dropping it into Blender or by downloading it and using Install from Disk. It is developed by Blendphys, with Clemens Barth as author, and the current version is 1.9.1, published in May 2024. Being GPL v3.0 or later, the source is available under that open-source license.
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