We have identified nano particles of different shapes (eg Ag NPs in rod shape, round, etc.). we wish to have computational study. Is it possible to draw the structures of nano particles or get them from any databases in .pdb or .mol, etc.?
jmol or any other crystal structure plotting program can take a variety of input formats, even lists of atoms as xyz coordinates. The common CIF format has the slight disadvantage that all atoms must be within a single unit cell. Thus a unit cell transformation is required that enlarges the original unit cell.
To build a list of atom coordinates, you should start from the atoms in the asymmetric unit, apply the space group symmetry and then expand the single unit cell to a large 3-D shape. If needed this shape can be cut into any desired form. The resulting list of atom coordinates can be exported in a suitable format.
Have a look at my DISCUS program that can do all these steps for you.
https://github.com/tproffen/DiffuseCode
As it is a huge program with many capacities beyond what you want I can help you with the specific needs
Reinhard Neder
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