Difference between revisions of "Jmol-Application/C3/Crystal-Structure-and-Unit-Cell/English-timed"

 

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! <center>Time</center>

! <center>Narration</center>

| 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 structure'''s of different crystal systems.  For example- '''Cubic''', '''Hexagonal '''and''' Rhombohedral.'''

| 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'''.

| '''Crystal structure'''s are grouped under seven crystal systems.

| 01:08

| This table shows the list of '''crystal system'''s and their corresponding '''lattice parameter'''s.

| 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.

| 02:36

| 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''',

| '''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:

| 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'''. .  

| 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.

| 04:51

| 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.  

| 05:14

| '''Unit cell''' of sodium chloride crystal opens on the '''screen'''.  

| 05:19

| '''Unit cell''' is the smallest repeating '''unit''' in a crystal.

| 05:29

| Back to the '''Jmol panel'''.

| 05:32

| Relevant data for '''unit cell''' is displayed on the left-hand side of the panel.

| 05:41

| 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 '''element'''s.

| 06:05

| We can also display '''block'''s of '''unit cell'''s 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.  

| 06:49

| Open the pop-up menu, go to '''symmetry''', go back to '''Reload {1 1 1}''' option.  

| 06:56

| To display the '''symmetry element'''s, 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'''

|* Open '''CIF''' in Jmol

|* Display '''unit cell''' and '''unit cell parameters'''

| 08:41

|* And display '''crystal structure'''s of '''sodium chloride''', '''graphite''' and '''calcite'''.

| 08:47

| For assignment:

Download '''CIF''' for quartz crystal from '''COD''' database.

| 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.

| This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.