How do I extract a molecular structure from a CIF file?

If the content of the .cif in question is fairly molecule-like, my recommendation are the cod-tools collection by the Crystallography Open Database. These may be obtained directly from their web site; if you use Debian 10/buster or Ubuntu 18.10LTS and higher, you equally find them in the the repositories (DebiChem tracker).

A typical extraction follows the pattern of

codcif2sdf input.cif > output.sdf

to write a new record (v2000 style). This works quite well, not only for .cif by the COD, but equally from other databases (including .cif the CSD file by CCDC if you forgot the direct export of .mol2 from the database), too. The cod-tools collection shines especially with unit cells of higher space group symmetries where a small number of unique atoms suffice to put the molecule together.

On occasion, an adjustment of bond orders may be necessary; e.g. in triazines like this one by COD where all six aromatic bonds between carbon and nitrogen are as double, instead as an aromatic bond.

If one has access to CCDC's Mercury app, the unique molecules (Z') can be easily written as mol2 or xyz files by the Save As option.

Of course, this requires completely written CIF file (with metadata). Often times, some codes lazily output all coordinates in the unit cell.

This is due to an unfortunate code-change in some versions of Open Babel. AFAIK, versions 3.0 and later have a heuristic to detect if the CIF contains a molecule, or is a traditional solid-state crystal structure (e.g., NaCl, YBCO, etc.). These versions are used by the latest development versions of Avogadro (1.93 / 1.94 at the moment).

Based on your screenshot, it looks like you're using Avogadro 1.x. There isn't a great way to back-fix this, since I'm not maintaining that code. (I'd much rather just get 2.0 finished and out the door.)

There are two work-arounds:

• Convert with Open Babel (e.g., CML, MDL, etc.) and read in that
• Use "fill unit cell" to get all atoms, and build a super-cell if needed.

The patch is here #1823, although it would probably be a pain to apply the patch, rebuild Avogadro 1.x with the older versions of Open Babel it uses, etc.

I tried out a few programs. It seems like Jmol and Molden do resolve the CIF structure and directly show me one molecule with all its bonds without requiring any further input.

Other programs like Avogadro or a command-line conversion with OpenBabel just produce the raw data of atoms scattered in the unit cell.

A command line package I use very often to convert between structure formats (and other things) is c2x. You can download the code from their website, and a quick "c2x --formats" suggests that it supports both cif files and xyz files.

If you're not tethered to Avogadro

You can use Mercury to change the system size by going to calculate, packing, and adjusting the cell size.

In the case of Avogadro, the process is really straightforward. Go to

File -> Save As

In the pop-up window, you can save the data as .xyz or .mol (among many others) types.