Published or almost published images

OmpA-like protein from P. gingivalis

Membrane anchor part of trimeric autotransporter adhesins…

… and its alignment

Aerolysin-like protein

DNA

More artistic representations

B-DNA:

Luciferase:

Hemoglobin:

Molecular manipulator designed by Dr. Drexler from imm.org.

Neisserial surface protein A (NspA)

Importing PDB file into Blender

Because it seems some of the readers may be interested in importing PDB file into Blender, here’s a short guide how to do it. Actually, there are two approaches to do it. First is represented by image of molecular manipulator, the second by image of NspA (two last pictures above).

Use pdb2blend script:

Download pdb2blend converter, open it in Blender and run it (Alt+P). Now, in the script window you can choose some options, like representation (balls, sticks and balls or sticks) or choose level of refinement. After import, the structure in chosen representation will appear in the 3D window with atoms colored according to schema in the script. There’s actually one caveat – spheres prepared with this script when rendered with ambient occlusion exhibit a weird pattern seen below. I’m not Blender expert so I have no idea how to solve it.

Second way of importing PDB structure into Blender in almost any representation is to use STL format. At least two molecular viewers are able to export structure in STL format: VMD and PMV (Python Molecular Viewer). I use PMV more often because it can export STL file with custom quality. Unfortunately, colors are not preserved in STL files from both programs (or Blender cannot read it, I’m not really sure). So, the you open PDB file in either of this programs, choose representation and then export/save as STL (in VMD this option is available under “Render”). After import the only thing left is to remove double vertices (edit mode, select all, edit -> vertices -> remove doubles). Voilla. You have molecular structures inside Blender.