[ase-users] From CIF files to XYZ

[Landi, Alessandro]

Hello everyone.


I am using ASE to read some CIF files and (among other things) to convert the structure in xyz format.


However using the following commands:


ase.io.read('filename.cif', atoms_ase)
ase.io.write('filename.xyz', atoms_ase)

I obtain a wrong structure, since the molecules need to be reconnected. This happens for all the molecules I have tested (about 20).

Could you please explain me what I am doing wrong?

If could be of any help, I attached an example:
"pentacene.cif" is the cif file that I give as input to ASE;
"pentacene.xyz" is the xyz file written by ASE;
"realstructure.xyz" is the structure of the reconnected molecules (obtained using CCDC Mercury)

Best regards,
Alessandro

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