Import from cif. Atomic positions

Yurii_Klysko · October 22, 2020, 8:50pm

Dear community members,
I’m trying to import crystal structure from .cif file in avogadro2 (1.93).
Cell parameters are read correctly. But there is a problem with atoms - all atomic coordinates are zero . The number of atoms and their names (types) are present.
I tried to import several .cif files, from several databases, but I didn’t succeed.
Did somebody face the same problem? please, help. Or any suggestions?

ghutchis · October 23, 2020, 3:01pm

Definitely weird.

What version of Open Babel do you have installed?
Can you post a link to the file?

I regularly use CIF from the COD with little problem.

Yurii_Klysko · October 23, 2020, 3:27pm

Hi,

Open Babel 3.0.0
as an example - http://www.crystallography.net/cod/4130301.html

ghutchis · October 23, 2020, 4:03pm

I think the problem is the older version of Open Babel. IIRC there was a bug in the CIF reader, which is fixed in 3.1.x.