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

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(Created page with " {| border = 1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Crystal Structure and unit cell''' in '''Jmol.''' |- | 00:07...")
 
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|  In this tutorial, we will learn to, Download '''CIF '''that is '''Crystallographic Information file''' from '''Crystallography Open Database.'''
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|  In this tutorial, we will learn to download '''CIF, '''that is, '''Crystallographic Information file''' from '''Crystallography Open Database.'''
  
 
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|  To follow this tutorial you should have Knowledge of high school chemistry.
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|  To follow this tutorial, you should have Knowledge of high school chemistry
  
 
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| And familiar with operations from Jmol window.  
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| and familiar with operations from Jmol window.  
 
   
 
   
 
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|  To record this tutorial, I am using, Ubuntu Operating System version 14.04
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|  To record this tutorial, I am using:* '''Ubuntu Operating System''' version '''14.04'''
  
 
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| Jmol version 12.2.32
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|* '''Jmol''' version '''12.2.32'''
  
 
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|* '''Java''' version '''7''' and  
  
 
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|* '''Mozilla Firefox browser 35.0'''
  
 
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|  Crystal structures are grouped under seven crystal systems.
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|  '''Crystal structure'''s are grouped under seven crystal systems.
  
 
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| This table shows the list of crystal systems and their corresponding lattice parameters.
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| This table shows the list of '''crystal system'''s and their corresponding '''lattice parameter'''s.
  
 
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|  To display the crystal structure on Jmol panel:
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|  To display the crystal structure on Jmol panel,
  
 
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| We need to download the Crystallographic Information File of a particular crystal.
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| we need to download the '''Crystallographic Information File''' of a particular crystal.
  
 
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| '''CIF''' format has the file extension '''.cif.'''
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| '''CIF''' format has the file extension ".cif".
  
 
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|  Here I have opened the '''COD''' website.
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|  Here, I have opened the '''COD''' website.
  
 
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|  Click on '''Search''' option. A new page opens.
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|  Click on '''Search''' option. A new '''page''' opens.
  
 
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|On the '''Search''' page we find many options to search for CIF files.  
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|On the '''Search''' page, we find many options to search for ''CIF' files.  
  
 
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|  Click on '''Hints and Tips''' link.
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|  Click on '''hints and tips''' link.
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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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|  Go back to the Search page.
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|  Go back to the '''Search''' page.
  
 
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|  We can search for the crystal structure using  '''COD ID'''
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|  We can search for the crystal structure using  '''COD ID''',
  
 
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| '''OpenBabel Fastsearch''' or  Type the name of the chemical or mineral in the '''text box'''.
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| '''OpenBabel Fastsearch''' or  type the name of the chemical or mineral in the text-box.
  
 
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|  For example to search for the CIF file of Sodium Chloride:
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|  For example, to search for the CIF file of Sodium Chloride:
  
 
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|  Type “'''Halite'''” which is the mineral name for sodium chloride, in the text box.
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|  Type “Halite” which is the mineral name for sodium chloride, in the text-box.
  
 
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|  Scroll down to '''elements '''box.
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|  Scroll-down to '''elements '''box.
  
 
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| Type the symbol for Sodium that is Na and Cl for chloride.
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| Type the symbol for Sodium, that is, Na and Cl for chloride.
  
 
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|  Scroll down to, '''Number of distinct elements''' box.
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|  Scroll-down to '''"Number of distinct elements.."''' box.
  
 
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|  Type 2 in the minimum box, if you want crystal structure with only two elements.That is '''Sodium''' and '''Chloride''' .  
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|  Type '2' in the minimum box, if you want crystal structure with only two elements, that is, '''Sodium''' and '''Chloride'''. .  
  
 
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|  Right click on the COD ID and click on “'''open the link in a new tab'''”.
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|  Right-click on the '''COD ID''' and click on “'''open the link in a new tab'''”.
  
 
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| A dialogue box opens on the screen, Select '''Open with''' option. Click on '''OK''' button.
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| A dialogue-box opens on the screen. Select '''Open with''' option. Click on '''OK''' button.
  
 
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Revision as of 16:11, 8 February 2016

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.
02:59 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 Conducts 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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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