extract asymmetric fragment

[job314]

I have this 600 atom Ih symmetry molecular cage. I am seeking help extracting the asymmetric unit from it to enter into CRYSTAL so I can use Ih symmetry. If anybody could help me with it, I would appreciate it.

B60C300H120O120[Ih].txt

JB

[aerba]

Hi,

Jefferson Maul has managed to generate this .cif file with 4 symmetry operators. As you suggest, there are probably more but this is what he could extract so far.

Beautiful system by the way: looks like a Christmas tree bauble!

[job314]

very grateful

[dmitoli]

Dear Jonas,

I tried using pymatgen to extract the point-symmetry information from your .xyz file (see the Python script below):

from pymatgen.core import Molecule
from pymatgen.symmetry import analyzer

bigstructure = Molecule.from_file("yourfile.xyz")
PGstructure = analyzer.PointGroupAnalyzer(bigstructure)
sym_mol = PGstructure.get_equivalent_atoms()

print(sym_mol["eq_sets"])

This returns a Python data structure containing the symmetry-irreducible sets of atoms (only 6 for this system!).
When preparing the CRYSTAL input, be careful with the orientation of your asymmetric unit. In my case, for example, I had to change the sign of the x and y coordinates to make the symmetry consistent with CRYSTAL’s conventions.
This is the .d12 file I was able to generate.

aerba Christmas is already in the air indeed!