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

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{|border=1
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{| border = 1
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|'''Time'''
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! <center>Time</center>
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| '''Narration'''
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! <center>Narration</center>
+
  
 
|-
 
|-
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| 00:01
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|00:01
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| Welcome to this tutorial on '''Crystal Structure and unit cell''' in '''Jmol.'''
+
|Welcome to this tutorial on '''Crystal Structure and unit cell''' in '''Jmol.'''
  
 
|-
 
|-
−
| 00:07
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|00:07
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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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| 00:17
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|00:17
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| Open '''CIF '''in Jmol.  
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|Open '''CIF '''in Jmol   
  
 
|-
 
|-
−
| 00:20
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|00:20
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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
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|00:25
−
| And display crystal structures of different crystal systems.  For example '''Cubic''', '''Hexagonal '''and''' Rhombohedral.'''
+
|And display '''crystal structure'''s of different crystal systems.  For example- '''Cubic''', '''Hexagonal '''and''' Rhombohedral.'''
  
 
|-
 
|-
 
|00:34
 
|00:34
−
| To follow this tutorial you should have Knowledge of high school chemistry.
+
|To follow this tutorial, you should have knowledge of high school chemistry
  
 
|-
 
|-
−
| 00:39
+
|00:39
−
| And familiar with operations from Jmol window.  
+
|and familiar with operations from '''Jmol window'''.  
 
   
 
   
 
|-
 
|-
−
| 00:42
+
|00:42
−
| If not, for relevant tutorials, please visit our website.  
+
|If not, for relevant tutorials, please visit our website.  
  
 
|-
 
|-
−
| 00:48
+
|00:48
−
| To record this tutorial, I am using, Ubuntu Operating System version 14.04
+
|To record this tutorial, I am using: * '''Ubuntu Operating System''' version '''14.04'''
  
 
|-
 
|-
−
| 00:54
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|00:54
−
| Jmol version 12.2.32
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|'''Jmol''' version '''12.2.32'''
  
 
|-
 
|-
−
| 00:57
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|00:57
−
| Java version 7 and  
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|'''Java''' version '''7''' and  
  
 
|-
 
|-
−
| 01:01
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|01:01
−
| Mozilla Firefox browser 35.0
+
|'''Mozilla Firefox browser 35.0'''.
  
 
|-
 
|-
 
|01:04
 
|01:04
−
| Crystal structures are grouped under seven crystal systems.
+
|'''Crystal structure'''s are grouped under seven crystal systems.
  
 
|-
 
|-
−
| 01:08
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|01:08
−
| This table shows the list of crystal systems and their corresponding lattice parameters.
+
|This table shows the list of '''crystal system'''s and their corresponding '''lattice parameter'''s.
  
 
|-
 
|-
Line 66: Line 65:
 
|-
 
|-
 
|01:20
 
|01:20
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| We will display crystal structures of '''Sodium chloride, Graphite '''and''' Calcite '''on''' Jmol panel'''.
+
|We will display crystal structures of '''Sodium chloride, Graphite '''and''' Calcite '''on''' Jmol panel'''.
  
 
|-
 
|-
−
| 01:27
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|01:27
−
| To display the crystal structure on Jmol panel:
+
|To display the crystal structure on Jmol panel,
  
 
|-
 
|-
−
| 01:31
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|01:31
−
| We need to download the Crystallographic Information File of a particular crystal.
+
|we need to download the '''Crystallographic Information File''' of a particular '''crystal'''.
  
 
|-
 
|-
−
| 01:37
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|01:37
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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.
  
 
|-
 
|-
−
| 01:43
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|01:43
−
| '''CIF''' format has the file extension '''.cif.'''
+
|'''CIF''' format has the file extension ".cif".
  
 
|-
 
|-
−
| 01:48
+
|01:48
−
| '''Crystallography Open Database''' is an open-access database.
+
|'''Crystallography Open Database''' is an open-access database.
  
 
|-
 
|-
−
| 01:53
+
|01:53
−
| The downloadable '''CIF''' are available at '''COD''' website.
+
|The downloadable '''CIF''' are available at '''COD''' website.
  
 
|-
 
|-
−
| 01:58
+
|01:58
−
| The website can be accessed through the given link.
+
|The website can be accessed through the given link.
  
 
|-
 
|-
−
| 02:03
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|02:03
−
| Let us open '''COD''' database website and download some''' CIF''' files.
+
|Let us open '''COD''' database website and download some''' CIF''' files.
  
 
|-
 
|-
−
| 02:10
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|02:10
−
| Here I have opened the '''COD''' website.
+
|Here, I have opened the '''COD''' website.
  
 
|-
 
|-
−
| 02:13
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|02:13
−
| On the left side of the page, information is divided under various headings.
+
|On the left side of the '''page''', information is divided under various headings.
  
 
|-
 
|-
−
| 02:19
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|02:19
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| Under the heading '''Accessing COD Data,''' there are sub-headings like '''Browse''', '''Search''' etc.
+
|Under the heading '''Accessing COD Data,''' there are sub-headings like '''Browse''', '''Search''' etc.
  
 
|-
 
|-
−
| 02:27
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|02:27
−
| Click on '''Search''' option. A new page opens.
+
|Click on '''Search''' option. A new '''page''' opens.
  
 
|-
 
|-
 
|02:31
 
|02:31
−
|On the '''Search''' page we find many options to search for CIF files.  
+
|On the '''Search''' page, we find many options to search for ''CIF' files.  
  
 
|-
 
|-
−
| 02:36
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|02:36
−
| 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.
+
  
 
|-
 
|-
−
| 02:46
+
|02:46
−
| Go back to the Search page.
+
|Go back to the '''Search''' page.
  
 
|-
 
|-
−
| 02:59
+
|02:49
−
| We can search for the crystal structure using  '''COD ID'''
+
|We can search for the crystal structure using  '''COD ID''',
  
 
|-
 
|-
 
|02:54
 
|02:54
−
| '''OpenBabel Fastsearch''' or  Type the name of the chemical or mineral in the '''text box'''.
+
|'''OpenBabel Fastsearch''' or  type the name of the chemical or mineral in the text-box.
  
 
|-
 
|-
−
| 03:01
+
|03:01
−
| For example to search for the CIF file of Sodium Chloride:
+
|For example, to search for the '''CIF''' file of Sodium Chloride:
  
 
|-
 
|-
 
|03:06
 
|03:06
−
| Type “'''Halite'''” which is the mineral name for sodium chloride, in the text box.
+
|Type “Halite” which is the mineral name for sodium chloride, in the text-box.
  
 
|-
 
|-
−
| 03:12
+
|03:12
−
| Scroll down to '''elements '''box.
+
|Scroll down to '''elements '''box.
  
 
|-
 
|-
−
| 03:15
+
|03:15
−
| Type the symbol for Sodium that is Na and Cl for chloride.
+
|Type the symbol for Sodium, that is, '''Na''' and '''Cl''' for chloride.
  
 
|-
 
|-
−
| 03:20
+
|03:20
−
| Scroll down to, '''Number of distinct elements''' box.
+
|Scroll down to '''"Number of distinct elements.."''' box.
  
 
|-
 
|-
−
| 03:24
+
|03:24
−
| Here we have an option to type minimum and maximum elements.  
+
|Here, we have an option to type minimum and maximum elements.  
  
 
|-
 
|-
−
| 03:29
+
|03:29
−
| Type 2 in the minimum box, if you want crystal structure with only two elements.That is '''Sodium''' and '''Chloride''' .  
+
|Type '2' in the minimum box, if you want crystal structure with only two elements, that is, '''Sodium''' and '''Chloride'''. .  
  
 
|-
 
|-
 
|03:37
 
|03:37
−
| Click on '''Send''' button.
+
|Click on '''Send''' button.
  
 
|-
 
|-
−
| 03:40
+
|03:40
−
| A web page opens with crystal structure data files for Sodium chloride.
+
|A web-page opens with crystal structure data files for Sodium chloride.
  
 
|-
 
|-
−
| 03:45
+
|03:45
−
| Right click on the COD ID and click on “'''open the link in a new tab'''”.
+
|Right-click on the '''COD ID''' and click on “'''open the link in a new tab'''”.
  
 
|-
 
|-
−
| 03:51
+
|03:51
−
| This page has detailed information regarding the particular crystal structure.  
+
|This page has detailed information regarding the particular crystal structure.  
  
 
|-
 
|-
−
| 03:57
+
|03:57
−
| Go back to the database web page.
+
|Go back to the database web page.
  
 
|-
 
|-
−
| 04:00
+
|04:00
−
| 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.  
  
 
|-
 
|-
−
| 04:08
+
|04:08
−
| A dialogue box opens on the screen, Select '''Open with''' option. Click on '''OK''' button.
+
|A dialog-box opens on the '''screen'''. Select '''Open with''' option. Click on '''OK''' button.
  
 
|-
 
|-
−
| 04:17
+
|04:17
−
| A folder with many '''CIF '''files for sodium chloride crystal opens on the screen.
+
|A folder with many '''CIF '''files for sodium chloride crystal opens on the screen.
  
 
|-
 
|-
−
| 04:23
+
|04:23
−
| Select the files you want to download by clicking on them.
+
|Select the files you want to download by clicking on them.
  
 
|-
 
|-
−
| 04:28
+
|04:28
−
| Click on “'''Extract'''” button on the tool bar.
+
|Click on “'''Extract'''” button on the tool bar.
  
 
|-
 
|-
−
| 04:32
+
|04:32
−
| Save the files at a convenient location on your system.
+
|'''Save''' the files at a convenient location on your system.
  
 
|-
 
|-
−
| 04:37
+
|04:37
−
| Click on '''Extract. '''Close the window.
+
|Click on '''Extract. '''Close the window.
  
 
|-
 
|-
−
| 04:41
+
|04:41
−
| Go back to the search page.
+
|Go back to the '''Search''' page.
  
 
|-
 
|-
 
|04:43
 
|04:43
−
|Now download '''CIF''' files for '''graphite''' and '''calcite''' using same procedure as before.
+
|Now, download '''CIF''' files for '''graphite''' and '''calcite''' using same procedure as before.
  
 
|-
 
|-
−
| 04:51
+
|04:51
−
| We will now open the '''CIF''' file of '''sodium chloride''' in Jmol.
+
|We will now open the '''CIF''' file of '''sodium chloride''' in Jmol.
  
 
|-
 
|-
−
| 04:55
+
|04:55
−
| Here I have opened the Jmol window.
+
|Here, I have opened the '''Jmol window'''.
  
 
|-
 
|-
−
| 04:59
+
|04:59
−
| Click on “Open a file” icon in the tool bar.
+
|Click on “Open a file” icon in the tool bar.
  
 
|-
 
|-
−
| 05:03
+
|05:03
−
| Navigate to the location of the '''CIF''' file of '''sodium chloride.''' which we have downloaded from the '''COD''' database.  
+
|Navigate to the location of the '''CIF''' file of '''sodium chloride''' which we have downloaded from the '''COD''' database.  
  
 
|-
 
|-
Line 243: Line 240:
  
 
|-
 
|-
−
| 05:14
+
|05:14
−
| '''Unit cell''' of sodium chloride crystal opens on the screen.  
+
|'''Unit cell''' of sodium chloride crystal opens on the '''screen'''.  
  
 
|-
 
|-
−
| 05:19
+
|05:19
−
| '''Unit cell''' is the smallest repeating unit in a crystal.
+
|'''Unit cell''' is the smallest repeating '''unit''' in a crystal.
  
 
|-
 
|-
 
|05:23
 
|05:23
−
|Stacking 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'''.
  
 
|-
 
|-
−
| 05:29
+
|05:29
−
| Back to the Jmol Panel.
+
|Back to the '''Jmol panel'''.
  
 
|-
 
|-
−
| 05:32
+
|05:32
−
| Relevant data for unit cell is displayed on the left-hand side of the panel.
+
|Relevant data for '''unit cell''' is displayed on the left-hand side of the panel.
  
 
|-
 
|-
Line 267: Line 264:
  
 
|-
 
|-
−
| 05:41
+
|05:41
−
| Sodium Chloride belongs to the cubic lattice system. Hence the vectors''' a''', '''b''' and''' c '''are equal.
+
|Sodium Chloride belongs to the '''cubic lattice system'''. Hence the vectors 'a', 'b' and 'c' are equal.
  
 
|-
 
|-
−
| 05:50
+
|05:50
−
| The angles '''alpha''', '''beta''' and '''gamma''' are 90 degrees.
+
|The angles '''alpha''', '''beta''' and '''gamma''' are 90 degrees.
  
 
|-
 
|-
−
| 05:55
+
|05:55
−
| Right click to open the pop-up menu.
+
|Right-click to open the '''pop-up menu'''.
  
 
|-
 
|-
−
| 05:59
+
|05:59
−
| Scroll down to '''Symmetry''' option.  
+
|Scroll-down to '''Symmetry''' option.  
  
 
|-
 
|-
−
| 06:01
+
|06:01
−
| In the sub-menu we have options to display symmetry elements.
+
|In the sub-menu, we have options to display symmetry '''element'''s.
  
 
|-
 
|-
−
| 06:05
+
|06:05
−
| We can also display blocks of unit cells using the options in the sub-menu.
+
|We can also display '''block'''s of '''unit cell'''s using the options in the sub-menu.
  
 
|-
 
|-
−
| 06:10
+
|06:10
−
| For example click on '''Reload {1 1 1}''' option.  
+
|For example, click on '''Reload {1 1 1}''' option.  
  
 
|-
 
|-
−
| 06:15
+
|06:15
−
| On the panel we have a unit cell block, showing face center cubic lattice.
+
|On the panel, we have a unit cell block, showing '''face center cubic lattice'''.
  
 
|-
 
|-
−
| 06:21
+
|06:21
−
| To change the display; Open the pop-up menu, scroll down to style then scheme and click on '''CPK Spacefil'''l.
+
|To change the display- open the pop-up menu, scroll down to '''Style''', then '''Scheme''' and click on '''CPK Spacefill'''.
  
 
|-
 
|-
−
| 06:29
+
|06:29
−
| Here on the panel we have the crystal structure in CPK display.
+
|Here, on the panel, we have the crystal structure in '''CPK''' display.
  
 
|-
 
|-
−
| 06:34
+
|06:34
−
| Open the pop-up menu again scroll down to symmetry and click on '''Reload {4 4 4 6 6 6 1}'''option.  
+
|Open the pop-up menu again, scroll-down to '''symmetry''' and click on '''Reload {4 4 4 6 6 6 1}''' option.  
  
 
|-
 
|-
 
|06:44
 
|06:44
−
|This option loads the 27 cell block on Jmol panel.
+
|This option '''load'''s the 27 cell block on Jmol panel.
  
 
|-
 
|-
−
| 06:49
+
|06:49
−
| Open the pop-up menu go to symmetry go back to '''Reload {1 1 1}''' option.  
+
|Open the pop-up menu, go to '''symmetry''', go back to '''Reload {1 1 1}''' option.  
  
 
|-
 
|-
−
| 06:56
+
|06:56
−
| To display the symmetry elements, open the pop-up menu again.
+
|To display the '''symmetry element'''s, open the pop-up menu again.
  
 
|-
 
|-
−
| 07:00
+
|07:00
−
| Scroll down to symmetry in the sub-menu and click on '''mirrorplane (x z y)''' option .
+
|Scroll down to '''Symmetry''' in the sub-menu and click on '''mirrorplane (x z y)''' option.  
  
 
|-
 
|-
−
| 07:08
+
|07:08
−
| On the panel we have a cubic lattice with '''mirrorplane (x z y)''' displayed.
+
|On the panel, we have a '''cubic lattice''' with '''mirrorplane (x z y)''' displayed.
  
 
|-
 
|-
−
| 07:16
+
|07:16
−
| Let us now load the CIF file for '''graphite''' ,which belongs to hexagonal crystal system.
+
|Let us now '''load''' the CIF file for '''graphite''' which belongs to '''hexagonal crystal system'''.
  
 
|-
 
|-
−
| 07:22
+
|07:22
−
| 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.
  
 
|-
 
|-
−
| 07:29
+
|07:29
−
| '''Unit cell''' for '''graphite''' opens on the panel.
+
|'''Unit cell''' for '''graphite''' opens on the panel.
  
 
|-
 
|-
−
| 07:33
+
|07:33
−
| Observe the unit cell parameters,
+
|Observe the unit cell parameters:
  
 
|-
 
|-
−
| 07:35
+
|07:35
−
| The vectors''' a '''equal to '''b''' but not equal to '''c.'''
+
|The vectors- 'a' equal to 'b' but not equal to 'c'.  
  
 
|-
 
|-
−
| 07:40
+
|07:40
−
| Angles, '''alpha''' and '''beta''' equal to 90 degrees and''' gamma '''equal to 120 degrees.
+
|Angles- '''alpha''' and '''beta''' equal to 90 degrees and''' gamma '''equal to 120 degrees.
  
 
|-
 
|-
−
| 07:47
+
|07:47
−
| Open the pop-up menu scroll down to '''Symmetry '''and click on '''Reload {444 666 1}''' option.
+
|Open the pop-up menu, scroll down to '''Symmetry '''and click on '''Reload {444 666 1}''' option.
  
 
|-
 
|-
−
| 07:56
+
|07:56
−
| '''Hexagonal lattice''' arrangement of atoms is shown on the screen.
+
|'''Hexagonal lattice''' arrangement of atoms is shown on the screen.
  
 
|-
 
|-
−
| 08:01
+
|08:01
−
| To change the display , open the pop-up menu go to style, go to scheme click on '''wireframe '''option.
+
|To change the display: open the pop-up menu, go to '''Style''', go to '''scheme''', click on '''Wireframe '''option.
  
 
|-
 
|-
−
| 08:10
+
|08:10
−
| 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.
  
 
|-
 
|-
−
| 08:16
+
|08:16
−
| '''Calcite''' belongs to the '''rhombohedral''' crystal system.
+
|'''Calcite''' belongs to the '''rhombohedral''' crystal system.
  
 
|-
 
|-
−
| 08:20
+
|08:20
−
| 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.
  
 
|-
 
|-
−
| 08:27
+
|08:27
−
| Let's summarize, In this tutorial we have learnt to  Download '''CIF''' from '''Crystallography Open Database.'''
+
|Let's summarize. In this tutorial, we have learnt to: * Download '''CIF''' from '''Crystallography Open Database'''
  
 
|-
 
|-
 
|08:35
 
|08:35
−
| Open '''CIF''' in Jmol.
+
|Open '''CIF''' in Jmol
  
 
|-
 
|-
 
|08:38
 
|08:38
−
|Display '''unit cell''' and '''unit cell parameters.'''
+
|Display '''unit cell''' and '''unit cell parameters'''
  
 
|-
 
|-
−
| 08:41
+
|08:41
−
| And display crystal structures of '''sodium chloride''', '''graphite''' and '''calcite'''.
+
|And display '''crystal structure'''s of '''sodium chloride''', '''graphite''' and '''calcite'''.
  
 
|-
 
|-
−
| 08:47
+
|08:47
−
| For assignment
+
|For assignment:Download '''CIF''' for quartz crystal from '''COD''' database.
−
 
+
−
Download '''CIF''' for quartz crystal from '''COD''' database.
+
  
 
|-
 
|-
 
|08:53
 
|08:53
−
|Display unit cell on '''Jmol''' panel and explore the symmetry options.
+
|Display '''unit cell''' on '''Jmol''' panel and explore the symmetry options.
  
 
|-
 
|-
−
| 08:59
+
|08:59
−
| This video summarizes the Spoken Tutorial project
+
|This video summarizes the '''Spoken Tutorial''' project.
  
 
|-
 
|-
−
| 09:02
+
|09:02
−
| If you do not have good bandwidth, you can download and watch it.  
+
|If you do not have good bandwidth, you can download and watch it.  
  
 
|-
 
|-
−
| 09:06
+
|09:06
−
| We Conducts workshops using spoken tutorials and Give certificates.
+
|We conduct workshops using spoken tutorials and give certificates. Please contact us.
−
 
+
−
Please contact us.
+
  
 
|-
 
|-
−
| 09:12
+
|09:12
−
| The spoken tutorial project is funded by NMEICT-MHRD govt of India.
+
|The spoken tutorial project is funded by NMEICT-MHRD govt of India.
  
 
|-
 
|-
 
|09:18
 
|09:18
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|This is Snehalatha from '''IIT Bombay''', signing off. Thank you for joining.  
−
 
+
 
|}
 
|}

Latest revision as of 15:34, 28 October 2020

Time Narration
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.
02:49 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 dialog-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.
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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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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