When I open a CIF file of a crystal structure in a typical molecular editor like Avogadro, then I just see a few symmetry-unique atoms scattered around the unit cell. But I don't see the full molecule with all its bonds. What is the easiest way to extract one individual molecular image with all its bonds from a cif file?
The two problems are:
- Some atoms are not shown at all if they are not symmetry-unique.
- Even if all the atoms are shown, then chemical bonds may go between the images in different unit cells, so that bonds are not properly displayed within the unit cell.
Let me show a screenshot below:
What I would like to happen is that the part with the orange atoms is moved up one unit cell, so that the carbon atoms attach to the blue nitrogen atoms shown at the top. Similarly all the scattered hydrogens have to be moved to different unit cells so that they attach to the atoms properly. This is clearly not a trivial task but it is something that would be needed whenever a CIF file is opened.