Fellow Jmol'ers:
As an example of filling a unit cell, see:http://macxray.chem.upenn.edu/cells/cell3148b.html
The researcher who had this structure done (it's a double carborane cage bonded to a niobium atom which has a chlorine attached, if anyone's interested) wanted to see if there were any interactions between CL's on neighboring molecules (sometimes these kind of molecules form dimers by forming a CL-CL bond). The model was built in a crystallographic program that constructs all the molecules with coordinates between x = -0.5 to +1.5, y = -0.1 to +1.1, z = -0.5 to +1.5 and then writes a PDB file. The limits on x, y and z can be adjusted interactively and, of course, the space group symmetry operations are used to build additional molecules starting with the asymmetric unit. The advantage of Jmol is that if I drew a hard copy paper representation of the packing diagram, the researcher may not "see" just what he's looking for, but by rotating the display in real time, it's easy for him. Also, certainly, the same thing could be done with many applications (RasMol, CrystMol, WebLabViewer), but then I need to get individual researchers trained in using whichever of those programs they have AND I have to deal with what kind of computer they have, etc. By just putting it on my webpage, I avoid all those problems.
I also saw a question about nomenclature of the molecules in an extended unit cell drawing. The very popular graphics program ORTEP invented a nomenclature many years ago to do this. This nomenclature has three parts: XXXYYYZZ. The no. XXX is the number of the atom in the asymmetric unit, YYY is a unit cell designation - the "central" unit cell is 555; the unit cell translated one unit cell length in the negative x direction is 455; the unit cell translated two unit cell lengths in the positive y direction and one unit cell in the negative z direction is 574. Finally, the ZZ no. is the number of the symmetry related position in the space group. Thus, for example, atom no. 36 that was produced by the third symmetry operation and then moved into the above unit cell is 3657403.
BTW, in constructing that packing diagram on my webpage, I'm unable to select boron atoms or niobium atoms using script commands in order to change their colors; I am able to select chlorines!
Pat
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