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I am doing research with calcium carbonate structures. I need a way in which I can familiarize myself with the lattice structure of calcium carbonate polymorphs, especially calcite.

I really struggle to see things in three dimensions. I borrowed an atomic model kit from my professor and that worked out OK, but I still wouldn't be able to tell which is the $(101)$ plane, for example.

I tried downloading software such as BallVIEW, but I found it quite confusing. I need something in which, I can load the structure, and then it can tell me where each $(hkl)$ plane lies. I don't know how to program so I would really appreciate it if anyone can direct me to something user-friendly.

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  • $\begingroup$ Perhaps CrystalMaker. $\endgroup$ – A.K. Jul 13 '18 at 3:22
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Mercury (available on Windows, Linux, MacOS) has a free version and is arguably the best crystallographic viewer for beginners. It also allows to add as many $(hkl)$ planes as you want. I used the structure of calcite from COD (1010962.cif).

Open your CIF file; by default Mercury loads an asymmetric unit. Once the CIF is loaded, go to Calculate → Packing/Slicing... and tick Pack option. Alternatively, tweak the volume populated by the atoms if needed. (This also automatically populates the list of planes with the planes denoting BFDH crystal morphology.)

Packing

Navigate to Calculate → Planes... → New Plane... → hkl and add the planes by Miller indices:

hkl dialogue

and, if needed, BFDH planes one by one:

BFDH planes

If you have CSD-Materials (paid option), then you'll be able to display BFDH theoretical crystal morphologies at once by going to CSD-Materials → Calculations → BFDH Morphology...; on export you'll get something like this:

Paywalled option


Alternatively, there is KrystalShaper (Windows only), a free lightweight program made specifically for displaying crystal morphologies:

KrystalShaper

P. S. Thanks to Buttonwood for useful comments regarding graphical details and reminding about BFDH crystal morphology.

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  • $\begingroup$ Sorry, incomplete. At least amend the display of the molecular structure and the calculated planes either by displaying the parallelepiped of the unit cell (Display -> Toolbars -> Display Options -> Show cell axes). Alternatively, if the OP is interested to relate the orientation of the molecules to the habit of crystal, to compute e.g. the BFDH morphology of the crystal and to visualize this on top (e.g., bip.weizmann.ac.il/course/structbioinfo/databases/CCDC_Mercury/…) by the materials module of Mercury (enterprise version, typically with the csd data base). $\endgroup$ – Buttonwood Jan 16 at 22:02
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    $\begingroup$ @Buttonwood Ehhm, the unit cell is present and is packed (probably it's hard to see, I'll think about better representation, maybe grow the whole thing a bit more); the OP didn't ask anything about morphology, so I showed the basic principle of illustrating an arbitrary plane using Miller indices. $\endgroup$ – andselisk Jan 16 at 22:08
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    $\begingroup$ Hard to see, indeed, the three-colour red-green-blue of a, b, and c axis, but there is a white cage of an epiped. A direct figure export (save as *.png) from the program about the second representation instead of a screen photo including the already presented GUI may be useful. Perhaps a stick-only model instead of ball-and-stick is advantageous, too. The morphology relation, introduced by "if" assumed the OP might become interested about this at a later point of research. $\endgroup$ – Buttonwood Jan 16 at 22:20
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There appear to be a variety of programs these days. Most I haven't tried, so take with a grain of salt (the last program I used was for DOS and I bought it in the early 1990s. I guess I'm old now. Sigh).

VESTA is free for academic use.

CrystalMaker requires a paid license.

List of other programs can be found here.

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