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, which is indeed of Ih point group!).
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.
Icosahedral point groups are available in CRYSTAL (Ih is point group number 47 in CRYSTAL), so the input fort this molecular cage reads:

Symm. structure 
MOLECULE
47
6
8       2.605032231   -11.914271806    11.762689798
6       4.344538598    15.664236912     4.366798884
6       3.427479683    14.428996321     8.326818862
6      -8.906580884     1.370529673    14.411150640             
1       2.632960331    14.962480562     7.832453804    
5      -8.776255231    -2.916256114    14.200279302     
COORPRT
TESTGEOM
END

aerba Christmas is already in the air indeed!