Here are some further comments, hints and tricks:
- You can discuss the script in this this forum (PDB) and here (XYZ).
- If you want to represent vacancies use an 'X' for the element name in the PDB file. For instance, write:
HETATM 125 X 11.260 11.260 5.630 1.00 1.00 X
Blender represents vacancies as transparent 3D cubes.
- If you want to build surfaces of crystals you can use the program Vesta, which is a free program. Build the unit cell of the crystal (you need the relative atom positions in the unit cell and the symmetry group) and enlarge the cell into x, y and z direction. Save this as a PDB file so that you can load it into Blender with help of Atomic Blender (PDB/XYZ).
- Probably you already know that there is a internet site (free access), which catalogues many biological molecules. The molecular structure of a molecule in PDB format can be downloaded: pdb.org
- Note that one big advantage of Atomic Blender (PDB/XYZ) is that the radius and color of one type of atom (e.g., all hydrogen atoms) can be selectively changed such that all other type of atoms (e.g., all carbon and oxygen atoms) remain unchanged (no grouping). See the options at the bottom of the panel. - The size (radius, etc.) of all atoms and sticks can be scaled at once, too.