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Atomic Blender - PDB file import/export                                   
2013-02-24

The addon Atomic Blender - PDB imports PDB (Protein Data Bank) files (*.pdb) into Blender. It reads the coordinates of all atoms in the PDB file and represents the atoms as balls in the Blender scene. Also the sticks, which connect atoms, 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 is interesting for scientists, who want to visualize their molecules, crystal structures, surfaces, etc. with Blender. The PDB format is widely distributed, and atomic structures such as molecules can be created with programs like CrystalMaker, Avogadro, Vesta and many others.

CrystalMaker
Vesta
Avogadro
http://www.crystalmaker.com/
http://jp-minerals.org/vesta/en/
http://avogadro.openmolecules.net/

Blender and the addon Atomic Blender - PDB can also be used in combination with the Atomic Simulation Environment (see here for more details):

Atomic Simulation Environment: https://wiki.fysik.dtu.dk/ase/

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.





























 

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