Last update: 2024-05-23
| The addon Atomic Blender (PDB/XYZ) imports PDB (Protein Data Bank) and XYZ files (*.pdb) into Blender. It reads the coordinates of all atoms in the PDB/XYZ file and represents the atoms as balls in the Blender scene. Also the sticks, which are described in PDB files, are shown if this option is chosen and if the sticks are listed in the PDB file. Many options can be chosen, which help to well represent the atoms and sticks. Objects or structures in a Blender 3D scene can also be exported. Atomic Blender (PDB/XYZ) is interesting for scientists, who want to visualize their molecules, crystal structures, surfaces, etc. with Blender. The PDB and XYZ formats are widely distributed, and atomic structures such as molecules can be created with programs like CrystalMaker, Avogadro, Vesta and many others. |
| CrystalMaker Vesta Avogadro |
Blender and Atomic Blender can also be used in combination with the Atomic Simulation Environment (see here for more details):
| Atomic Simulation Environment |
Thanks to Blender, fancy graphics of molecules, crystal structures, surfaces and complex atomic arrangements can be obtained. Such graphics meet the standards of top-level journals, which have an high impact factor. Please, read the general information about Blender before you use the addon.
Here is the typical structure of a PDB file:
| Identifier |
No. |
Element or identifier | x |
y |
z |
Element |
| HETATM or ATOM |
5 |
Cl |
-1.220 | 0.879 | -1.674 | Cl |
Some examples with corresponding PDB files can be found here.
Here is the typical structure of a XYZ ASCII file (3 atoms and 2 frames):
| 3 |
|||
| Some comments in this line |
|||
| Au | -8.160000 | 44.880000 | 2.040000 |
| Au |
38.760000 |
-8.160000 |
2.040000 |
| Au |
-10.200000 |
34.680000 |
2.040000 |
| 3 |
|||
| Some comments in this line | |||
| Au | -6.160000 | 44.880000 | 2.040000 |
| Au |
30.000000 |
-8.160000 |
2.040000 |
| Au |
-10.200000 |
38.000000 |
2.040000 |
See also here and read this xyz file.