Here are some further comments, hints and tricks:
- You can discuss the script in this forum: Forum at blenderartists.org
- 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 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.
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
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.