Difference between revisions of "Jmol-Application/C3/Crystal-Structure-and-Unit-Cell/English-timed"
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| − | | In this tutorial, we will learn to download '''CIF, '''that is, '''Crystallographic Information file''' from '''Crystallography Open Database | + | | In this tutorial, we will learn: * to download '''CIF, '''that is, '''Crystallographic Information file''' from '''Crystallography Open Database''' |
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| − | | Open '''CIF '''in Jmol | + | |* Open '''CIF '''in Jmol |
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| − | | Display '''unit cell''' and '''unit cell parameters '''on Jmol panel | + | |* Display '''unit cell''' and '''unit cell parameters '''on Jmol panel |
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| 00:25 | | 00:25 | ||
| − | | And display crystal structures of different crystal systems. For example '''Cubic''', '''Hexagonal '''and''' Rhombohedral.''' | + | |* And display crystal structures of different crystal systems. For example- '''Cubic''', '''Hexagonal '''and''' Rhombohedral.''' |
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| − | | To follow this tutorial, you should have | + | | To follow this tutorial, you should have knowledge of high school chemistry |
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| 00:39 | | 00:39 | ||
| − | | and familiar with operations from Jmol window. | + | | and familiar with operations from '''Jmol window'''. |
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| − | |* '''Mozilla Firefox browser 35.0''' | + | |* '''Mozilla Firefox browser 35.0'''. |
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| − | | '''CIF''' is a standard text file format for representing crystallographic information. | + | | '''CIF''' is a standard text file format for representing '''crystallographic''' information. |
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| − | | Click on '''hints and tips''' link. | + | | Click on '''hints and tips''' link. A page opens with information on how to use '''search''' options effectively. |
| − | A page opens with information on how to use search options effectively. | + | |
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| − | | For example, to search for the CIF file of Sodium Chloride: | + | | For example, to search for the '''CIF''' file of Sodium Chloride: |
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| − | | Scroll | + | | Scroll down to '''elements '''box. |
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| − | | Scroll | + | | Scroll down to '''"Number of distinct elements.."''' box. |
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| − | | A web page opens with crystal structure data files for Sodium chloride. | + | | A web-page opens with crystal structure data files for Sodium chloride. |
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| − | | Click on the link “'''archive of CIF files'''” located on the right-hand side of the page. | + | | Click on the link “'''archive of CIF files'''”, located on the right-hand side of the page. |
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| − | | '''Unit cell''' of sodium chloride crystal opens on the screen. | + | | '''Unit cell''' of sodium chloride crystal opens on the '''screen'''. |
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| − | |'''Stack'''ing of these unit cells in 3 dimensions will form the basis of the '''crystal structure'''. | + | |'''Stack'''ing of these unit cells in '''3''' dimensions will form the basis of the '''crystal structure'''. |
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| − | | Back to the Jmol | + | | Back to the '''Jmol panel'''. |
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| − | | We can also display | + | | We can also display '''block'''s of unit cells using the options in the sub-menu. |
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| − | | To change the display- open the pop-up menu, scroll | + | | To change the display- open the pop-up menu, scroll down to '''Style''', then '''Scheme''' and click on '''CPK Spacefill'''. |
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| − | | Here, on the panel, we have the crystal structure in CPK display. | + | | Here, on the panel, we have the crystal structure in '''CPK''' display. |
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| − | | Scroll | + | | Scroll down to '''Symmetry''' in the sub-menu and click on '''mirrorplane (x z y)''' option. |
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| − | | As shown earlier, use '''Open a file '''option to '''load''' the CIF file for graphite on the panel. | + | | As shown earlier, use '''Open a file '''option to '''load''' the '''CIF''' file for graphite on the panel. |
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| − | | The vectors | + | | The vectors- 'a' equal to 'b' but not equal to 'c'. |
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| − | | Angles | + | | Angles- '''alpha''' and '''beta''' equal to 90 degrees and''' gamma '''equal to 120 degrees. |
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| − | | Similarly, I have opened a CIF file of mineral '''calcite''' on the panel. | + | | Similarly, I have opened a '''CIF''' file of mineral '''calcite''' on the panel. |
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| − | | You can open the CIF of any crystal system and explore the structure and symmetry options. | + | | You can open the '''CIF''' of any crystal system and explore the structure and symmetry options. |
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| − | |Display unit cell on '''Jmol''' panel and explore the symmetry options. | + | |Display '''unit cell''' on '''Jmol''' panel and explore the symmetry options. |
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| − | | We conduct workshops using spoken tutorials and give certificates. | + | | We conduct workshops using spoken tutorials and give certificates. Please contact us. |
| − | Please contact us. | + | |
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Revision as of 15:56, 11 February 2016
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| 00:01 | Welcome to this tutorial on Crystal Structure and unit cell in Jmol. |
| 00:07 | In this tutorial, we will learn: * to download CIF, that is, Crystallographic Information file from Crystallography Open Database |
| 00:17 | * Open CIF in Jmol |
| 00:20 | * Display unit cell and unit cell parameters on Jmol panel |
| 00:25 | * And display crystal structures of different crystal systems. For example- Cubic, Hexagonal and Rhombohedral. |
| 00:34 | To follow this tutorial, you should have knowledge of high school chemistry |
| 00:39 | and familiar with operations from Jmol window. |
| 00:42 | If not, for relevant tutorials, please visit our website. |
| 00:48 | To record this tutorial, I am using:* Ubuntu Operating System version 14.04 |
| 00:54 | * Jmol version 12.2.32 |
| 00:57 | * Java version 7 and |
| 01:01 | * Mozilla Firefox browser 35.0. |
| 01:04 | Crystal structures are grouped under seven crystal systems. |
| 01:08 | This table shows the list of crystal systems and their corresponding lattice parameters. |
| 01:14 | Examples for crystals of various compounds and minerals are listed here. |
| 01:20 | We will display crystal structures of Sodium chloride, Graphite and Calcite on Jmol panel. |
| 01:27 | To display the crystal structure on Jmol panel, |
| 01:31 | we need to download the Crystallographic Information File of a particular crystal. |
| 01:37 | CIF is a standard text file format for representing crystallographic information. |
| 01:43 | CIF format has the file extension ".cif". |
| 01:48 | Crystallography Open Database is an open-access database. |
| 01:53 | The downloadable CIF are available at COD website. |
| 01:58 | The website can be accessed through the given link. |
| 02:03 | Let us open COD database website and download some CIF files. |
| 02:10 | Here, I have opened the COD website. |
| 02:13 | On the left side of the page, information is divided under various headings. |
| 02:19 | Under the heading Accessing COD Data, there are sub-headings like Browse, Search etc. |
| 02:27 | Click on Search option. A new page opens. |
| 02:31 | On the Search page, we find many options to search for CIF' files. |
| 02:36 | Click on hints and tips link. A page opens with information on how to use search options effectively. |
| 02:46 | Go back to the Search page. |
| 02:59 | We can search for the crystal structure using COD ID, |
| 02:54 | OpenBabel Fastsearch or type the name of the chemical or mineral in the text-box. |
| 03:01 | For example, to search for the CIF file of Sodium Chloride: |
| 03:06 | Type “Halite” which is the mineral name for sodium chloride, in the text-box. |
| 03:12 | Scroll down to elements box. |
| 03:15 | Type the symbol for Sodium, that is, Na and Cl for chloride. |
| 03:20 | Scroll down to "Number of distinct elements.." box. |
| 03:24 | Here, we have an option to type minimum and maximum elements. |
| 03:29 | Type '2' in the minimum box, if you want crystal structure with only two elements, that is, Sodium and Chloride. . |
| 03:37 | Click on Send button. |
| 03:40 | A web-page opens with crystal structure data files for Sodium chloride. |
| 03:45 | Right-click on the COD ID and click on “open the link in a new tab”. |
| 03:51 | This page has detailed information regarding the particular crystal structure. |
| 03:57 | Go back to the database web page. |
| 04:00 | Click on the link “archive of CIF files”, located on the right-hand side of the page. |
| 04:08 | A dialogue-box opens on the screen. Select Open with option. Click on OK button. |
| 04:17 | A folder with many CIF files for sodium chloride crystal opens on the screen. |
| 04:23 | Select the files you want to download by clicking on them. |
| 04:28 | Click on “Extract” button on the tool bar. |
| 04:32 | Save the files at a convenient location on your system. |
| 04:37 | Click on Extract. Close the window. |
| 04:41 | Go back to the Search page. |
| 04:43 | Now, download CIF files for graphite and calcite using same procedure as before. |
| 04:51 | We will now open the CIF file of sodium chloride in Jmol. |
| 04:55 | Here, I have opened the Jmol window. |
| 04:59 | Click on “Open a file” icon in the tool bar. |
| 05:03 | Navigate to the location of the CIF file of sodium chloride which we have downloaded from the COD database. |
| 05:12 | Click on Open. |
| 05:14 | Unit cell of sodium chloride crystal opens on the screen. |
| 05:19 | Unit cell is the smallest repeating unit in a crystal. |
| 05:23 | Stacking of these unit cells in 3 dimensions will form the basis of the crystal structure. |
| 05:29 | Back to the Jmol panel. |
| 05:32 | Relevant data for unit cell is displayed on the left-hand side of the panel. |
| 05:37 | It begins with the space group classification. |
| 05:41 | Sodium Chloride belongs to the cubic lattice system. Hence the vectors 'a', 'b' and 'c' are equal. |
| 05:50 | The angles alpha, beta and gamma are 90 degrees. |
| 05:55 | Right-click to open the pop-up menu. |
| 05:59 | Scroll-down to Symmetry option. |
| 06:01 | In the sub-menu, we have options to display symmetry elements. |
| 06:05 | We can also display blocks of unit cells using the options in the sub-menu. |
| 06:10 | For example, click on Reload {1 1 1} option. |
| 06:15 | On the panel, we have a unit cell block, showing face center cubic lattice. |
| 06:21 | To change the display- open the pop-up menu, scroll down to Style, then Scheme and click on CPK Spacefill. |
| 06:29 | Here, on the panel, we have the crystal structure in CPK display. |
| 06:34 | Open the pop-up menu again, scroll-down to symmetry and click on Reload {4 4 4 6 6 6 1} option. |
| 06:44 | This option loads the 27 cell block on Jmol panel. |
| 06:49 | Open the pop-up menu, go to symmetry, go back to Reload {1 1 1} option. |
| 06:56 | To display the symmetry elements, open the pop-up menu again. |
| 07:00 | Scroll down to Symmetry in the sub-menu and click on mirrorplane (x z y) option. |
| 07:08 | On the panel, we have a cubic lattice with mirrorplane (x z y) displayed. |
| 07:16 | Let us now load the CIF file for graphite which belongs to hexagonal crystal system. |
| 07:22 | As shown earlier, use Open a file option to load the CIF file for graphite on the panel. |
| 07:29 | Unit cell for graphite opens on the panel. |
| 07:33 | Observe the unit cell parameters: |
| 07:35 | The vectors- 'a' equal to 'b' but not equal to 'c'. |
| 07:40 | Angles- alpha and beta equal to 90 degrees and gamma equal to 120 degrees. |
| 07:47 | Open the pop-up menu, scroll down to Symmetry and click on Reload {444 666 1} option. |
| 07:56 | Hexagonal lattice arrangement of atoms is shown on the screen. |
| 08:01 | To change the display: open the pop-up menu, go to Style, go to scheme, click on Wireframe option. |
| 08:10 | Similarly, I have opened a CIF file of mineral calcite on the panel. |
| 08:16 | Calcite belongs to the rhombohedral crystal system. |
| 08:20 | You can open the CIF of any crystal system and explore the structure and symmetry options. |
| 08:27 | Let's summarize. In this tutorial, we have learnt to: * Download CIF from Crystallography Open Database |
| 08:35 | * Open CIF in Jmol |
| 08:38 | * Display unit cell and unit cell parameters |
| 08:41 | * And display crystal structures of sodium chloride, graphite and calcite. |
| 08:47 | For assignment:
Download CIF for quartz crystal from COD database. |
| 08:53 | Display unit cell on Jmol panel and explore the symmetry options. |
| 08:59 | This video summarizes the Spoken Tutorial project. |
| 09:02 | If you do not have good bandwidth, you can download and watch it. |
| 09:06 | We conduct workshops using spoken tutorials and give certificates. Please contact us. |
| 09:12 | The spoken tutorial project is funded by NMEICT-MHRD govt of India. |
| 09:18 | This is Snehalatha from IIT Bombay, signing off. Thank you for joining. |
