[ase-users] From CIF files to XYZ

[Oscar Xavier Guerrero]

Hello,

When you read the structure an Atoms object is created. You need to store
that object on a variable and then you can write that one. As so:

First read the data:
*from* ase.io *import* read, write
atoms = read('filename.cif')
Then write:
write('filename.xyz', atoms)
or you can use:
atoms.write('filename.xyz')




2017-12-08 12:19 GMT+00:00 Landi, Alessandro via ase-users <
ase-users at listserv.fysik.dtu.dk>:

> 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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