Welcome to this tutorial on Crystal Structure and unit cell in Jmol.
In this tutorial, we will learn: * to download CIF, that is, Crystallographic Information File from Crystallography Open Database
Open CIF in Jmol
Display unit cell and unit cell parameters on Jmol panel
And display crystal structures of different crystal systems. For example- Cubic, Hexagonal and Rhombohedral.
To follow this tutorial, you should have knowledge of high school chemistry
and familiar with operations from Jmol window.
If not, for relevant tutorials, please visit our website.
To record this tutorial, I am using: * Ubuntu Operating System version 14.04
Jmol version 12.2.32
Java version 7 and
Mozilla Firefox browser 35.0.
Crystal structures are grouped under seven crystal systems.
This table shows the list of crystal systems and their corresponding lattice parameters.
Examples for crystals of various compounds and minerals are listed here.
We will display crystal structures of Sodium chloride, Graphite and Calcite on Jmol panel.
To display the crystal structure on Jmol panel,
we need to download the Crystallographic Information File of a particular crystal.
CIF is a standard text file format for representing crystallographic information.
CIF format has the file extension ".cif".
Crystallography Open Database is an open-access database.
The downloadable CIF are available at COD website.
The website can be accessed through the given link.
Let us open COD database website and download some CIF files.
Here, I have opened the COD website.
On the left side of the page, information is divided under various headings.
Under the heading Accessing COD Data, there are sub-headings like Browse, Search etc.
Click on Search option. A new page opens.
On the Search page, we find many options to search for CIF' files.
Click on hints and tips link. A page opens with information on how to use search options effectively.
Go back to the Search page.
We can search for the crystal structure using COD ID,
OpenBabel Fastsearch or type the name of the chemical or mineral in the text-box.
For example, to search for the CIF file of Sodium Chloride:
Type “Halite” which is the mineral name for sodium chloride, in the text-box.
Scroll down to elements box.
Type the symbol for Sodium, that is, Na and Cl for chloride.
Scroll down to "Number of distinct elements.." box.
Here, we have an option to type minimum and maximum elements.
Type '2' in the minimum box, if you want crystal structure with only two elements, that is, Sodium and Chloride. .
Click on Send button.
A web-page opens with crystal structure data files for Sodium chloride.
Right-click on the COD ID and click on “open the link in a new tab”.
This page has detailed information regarding the particular crystal structure.
Go back to the database web page.
Click on the link “archive of CIF files”, located on the right-hand side of the page.
A dialogue-box opens on the screen. Select Open with option. Click on OK button.
A folder with many CIF files for sodium chloride crystal opens on the screen.
Select the files you want to download by clicking on them.
Click on “Extract” button on the tool bar.
Save the files at a convenient location on your system.
Click on Extract. Close the window.
Go back to the Search page.
Now, download CIF files for graphite and calcite using same procedure as before.
We will now open the CIF file of sodium chloride in Jmol.
Here, I have opened the Jmol window.
Click on “Open a file” icon in the tool bar.
Navigate to the location of the CIF file of sodium chloride which we have downloaded from the COD database.
Click on Open.
Unit cell of sodium chloride crystal opens on the screen.
Unit cell is the smallest repeating unit in a crystal.
Stacking of these unit cells in 3 dimensions will form the basis of the crystal structure.
Back to the Jmol panel.
Relevant data for unit cell is displayed on the left-hand side of the panel.
It begins with the space group classification.
Sodium Chloride belongs to the cubic lattice system. Hence the vectors 'a', 'b' and 'c' are equal.
The angles alpha, beta and gamma are 90 degrees.
Right-click to open the pop-up menu.
Scroll-down to Symmetry option.
In the sub-menu, we have options to display symmetry elements.
We can also display blocks of unit cells using the options in the sub-menu.
For example, click on Reload {1 1 1} option.
On the panel, we have a unit cell block, showing face center cubic lattice.
To change the display- open the pop-up menu, scroll down to Style, then Scheme and click on CPK Spacefill.
Here, on the panel, we have the crystal structure in CPK display.
Open the pop-up menu again, scroll-down to symmetry and click on Reload {4 4 4 6 6 6 1} option.
This option loads the 27 cell block on Jmol panel.
Open the pop-up menu, go to symmetry, go back to Reload {1 1 1} option.
To display the symmetry elements, open the pop-up menu again.
Scroll down to Symmetry in the sub-menu and click on mirrorplane (x z y) option.
On the panel, we have a cubic lattice with mirrorplane (x z y) displayed.
Let us now load the CIF file for graphite which belongs to hexagonal crystal system.
As shown earlier, use Open a file option to load the CIF file for graphite on the panel.
Unit cell for graphite opens on the panel.
Observe the unit cell parameters:
The vectors- 'a' equal to 'b' but not equal to 'c'.
Angles- alpha and beta equal to 90 degrees and gamma equal to 120 degrees.
Open the pop-up menu, scroll down to Symmetry and click on Reload {444 666 1} option.
Hexagonal lattice arrangement of atoms is shown on the screen.
To change the display: open the pop-up menu, go to Style, go to scheme, click on Wireframe option.
Similarly, I have opened a CIF file of mineral calcite on the panel.
Calcite belongs to the rhombohedral crystal system.
You can open the CIF of any crystal system and explore the structure and symmetry options.
Let's summarize. In this tutorial, we have learnt to: * Download CIF from Crystallography Open Database
Open CIF in Jmol
Display unit cell and unit cell parameters
And display crystal structures of sodium chloride, graphite and calcite.
For assignment:Download CIF for quartz crystal from COD database.
Display unit cell on Jmol panel and explore the symmetry options.
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