Difference between revisions of "Jmol-Application/C4/Symmetry-and-Point-Groups/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
(Created page with "{| Border =1 |<center>Time</center> | <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Symmetry and Point Group '''in Jmol'''.''' |- | 00:06 | In thi...")
 
Line 5: Line 5:
 
|-
 
|-
 
| 00:01
 
| 00:01
−
|  Welcome to this tutorial on '''Symmetry and Point Group '''in Jmol'''.'''
+
|  Welcome to this tutorial on '''Symmetry and Point Group '''in '''Jmol'''.
  
 
|-
 
|-
 
| 00:06
 
| 00:06
−
|  In this tutorial, we will learn to  
+
|  In this tutorial, we will learn to:
  
 
|-
 
|-
 
| 00:08
 
| 00:08
−
| Draw line, that is axis through atoms in a molecule.
+
|* Draw line, that is, axis through atoms in a molecule.
  
 
|-
 
|-
 
| 00:12
 
| 00:12
−
| Spin and rotate the molecule along the axis.
+
|* Spin and rotate the molecule along the axis.
  
 
|-
 
|-
 
| 00:17
 
| 00:17
−
| Draw plane through atoms in a molecule.
+
|* Draw plane through atoms in a molecule.
  
 
|-
 
|-
 
| 00:21
 
| 00:21
−
| And demonstrate point group classification.  
+
|* And demonstrate point group classification.  
  
 
|-
 
|-
 
|00:25
 
|00:25
−
| To follow this tutorial you should have, Knowledge of undergraduate Chemistry  and Familiar with operations from Jmol window.
+
| To follow this tutorial, you should have Knowledge of undergraduate Chemistry  and familiar with operations from '''Jmol window'''.
  
 
|-
 
|-
Line 37: Line 37:
 
|-
 
|-
 
| 00:39
 
| 00:39
−
|  To record this tutorial, I am using,
+
|  To record this tutorial, I am using:
  
 
|-
 
|-
 
| 00:42
 
| 00:42
−
| '''Ubuntu '''Operating System version. 14.04
+
|* '''Ubuntu '''Operating System version 14.04
  
 
|-
 
|-
 
| 00:46
 
| 00:46
−
| '''Jmol''' version 12.2.32
+
|* '''Jmol''' version 12.2.32
  
 
|-
 
|-
 
| 00:50
 
| 00:50
−
| '''Java''' version 7  and '''Mozilla Firefox browser '''35.0
+
|* '''Java''' version 7  and * '''Mozilla Firefox browser '''35.0
 
|-
 
|-
 
| 00:57
 
| 00:57
Line 56: Line 56:
 
|-
 
|-
 
| 01:03
 
| 01:03
−
| Axis of symmetry  
+
|* Axis of symmetry  
  
 
|-
 
|-
 
| 01:05
 
| 01:05
−
| Plane of symmetry
+
|* Plane of symmetry
  
 
|-
 
|-
 
| 01:06
 
| 01:06
−
| Center of symmetry etc
+
|* Center of symmetry etc.
  
 
|-
 
|-
 
| 01:09
 
| 01:09
−
| We will use Jmol to display these symmetry elements in a molecule.
+
| We will use '''Jmol''' to display these symmetry elements in a molecule.
  
 
|-
 
|-
 
| 01:14
 
| 01:14
−
|  Let us begin this tutorial by drawing C3 rotational axis through atoms in a model of methane.  
+
|  Let us begin this tutorial by drawing '''C3 rotational axis''' through atoms in a model of '''methane'''.  
  
 
|-
 
|-
Line 80: Line 80:
 
|-
 
|-
 
| 01:25
 
| 01:25
−
| Click on '''modelkit '''menu to get the ball and stick model of methane on the panel.
+
| Click on '''modelkit '''menu to get the '''ball and stick''' model of methane on the panel.
  
 
|-
 
|-
 
| 01:31
 
| 01:31
−
|  Label the atoms in the '''methane''' molecule by using display menu in the tool bar.
+
|  Label the atoms in the '''methane''' molecule by using '''Display''' menu in the tool bar.
  
 
|-
 
|-
 
|  01:37
 
|  01:37
−
|  Click on '''Display,''' scroll down to '''Label '''and Click on''' Number''' option.
+
|  Click on '''Display,''' scroll down to '''Label '''and click on''' Number''' option.
  
 
|-
 
|-
Line 100: Line 100:
 
|-
 
|-
 
| 01:53
 
| 01:53
−
|  To open the Console click on '''File''' menu.
+
|  To open the Console, click on '''File''' menu.
  
 
|-
 
|-
Line 116: Line 116:
 
|-
 
|-
 
| 02:10
 
| 02:10
−
|  Detailed information on Jmol script commands is available at this website.  
+
|  Detailed information on '''Jmol script commands''' is available at this website.  
  
 
|-
 
|-
Line 124: Line 124:
 
|-
 
|-
 
| 02:19
 
| 02:19
−
| A web page opens with a list of keywords used for writing script commands in Jmol.
+
| A web-page opens with a list of keywords used for writing script commands in Jmol.
  
 
|-
 
|-
 
| 02:26
 
| 02:26
−
|  Scroll down and Click on word '''draw '''in the list.
+
|  Scroll down and click on word '''draw '''in the list.
  
 
|-
 
|-
 
| 02:31
 
| 02:31
−
| A page opens with details about the '''draw '''keyword.  
+
| A '''page''' opens with details about the '''draw '''keyword.  
  
 
|-
 
|-
 
| 02:36
 
| 02:36
−
| A general syntax for the draw command is given at the top of the page.
+
| A general syntax for the '''draw''' command is given at the top of the '''page'''.
  
 
|-
 
|-
Line 144: Line 144:
 
|-
 
|-
 
|02:47
 
|02:47
−
|  Let us now go back to the Jmol panel.
+
|  Let us now go back to the '''Jmol panel'''.
  
 
|-
 
|-
Line 152: Line 152:
 
|-
 
|-
 
| 02:55
 
| 02:55
−
|  To draw a line that represents C3 rotational axis:  
+
|  To draw a line that represents '''C3 rotational axis''':  
  
 
|-
 
|-
Line 160: Line 160:
 
|-
 
|-
 
| 03:04
 
| 03:04
−
| The command line begins with the word “'''draw'''”, followed by object ID.
+
| The '''command line''' begins with the word “'''draw'''”, followed by object ID.
  
 
|-
 
|-
Line 172: Line 172:
 
|-
 
|-
 
| 03:18
 
| 03:18
−
| With in brackets atom number equal to 1 and atom number equal to 2. Press enter.  
+
| Within brackets atom number equal to 1 and atom number equal to 2. Press '''Enter'''.  
  
 
|-
 
|-
Line 192: Line 192:
 
|-
 
|-
 
| 03:41
 
| 03:41
−
| To draw C2 rotational axis: Type the following command in the console.
+
| To draw '''C2 rotational axis''': Type the following command in the console.
  
 
|-
 
|-
 
| 03:47
 
| 03:47
−
| In this command,the numbers in curly brackets indicate the Cartesian coordinates for the line.
+
| In this command, the numbers in curly brackets indicate the Cartesian coordinates for the line
  
 
|-
 
|-
 
| 03:54
 
| 03:54
−
| Followed by a command to specify the color of the line. Press enter.  
+
| followed by a command to specify the color of the line. Press '''Enter'''.  
  
 
|-
 
|-
 
| 03:59
 
| 03:59
−
|  Now on the panel we have methane with C2 and C3 rotational axes.
+
|  Now, on the panel, we have methane with C2 and C3 rotational axes.
  
 
|-
 
|-
 
| 04:05
 
| 04:05
−
|  To rotate along the line 1 that is C3 axis , type the following command  
+
|  To rotate along the line 1, that is C3 axis, type the following command.
  
 
|-
 
|-
 
| 04:12
 
| 04:12
−
| '''rotate $line1 60 ''' (rotate space dollar line1 space 60)
+
| '''rotate $line1 60 ''' (rotate space dollar line1 space 60).
  
 
|-
 
|-
 
| 04:18
 
| 04:18
−
| The number 60 refers to the degrees of rotation. Press enter.
+
| The number 60 refers to the degrees of rotation. Press '''Enter'''.
  
 
|-
 
|-
Line 224: Line 224:
 
|-
 
|-
 
| 04:27
 
| 04:27
−
|  To spin the molecule along '''line1''' type the following command.
+
|  To spin the molecule along '''line1''', type the following command.
  
 
|-
 
|-
 
| 04:32
 
| 04:32
−
| '''spin $line1 180 60''' '''(spin space dollar line1 space 180 space 60)'''
+
| '''spin $line1 180 60''' '''(spin space dollar line1 space 180 space 60)'''.
  
 
|-
 
|-
 
| 04:39
 
| 04:39
−
| The number 180 refers to degrees of rotation and 60 refers to the speed of rotation. Press enter.
+
| The number 180 refers to degrees of rotation and 60 refers to the speed of rotation. Press '''Enter'''.
  
 
|-
 
|-
 
| 04:48
 
| 04:48
−
|  On panel we see the '''methane''' model spin along '''line1''', that is C3 axis.  
+
|  On panel, we see the '''methane''' model spin along '''line1''', that is C3 axis.  
  
 
|-
 
|-
 
| 04:55
 
| 04:55
−
|  As an assignment
+
|  As an assignment-
  
 
|-
 
|-
 
| 04:56
 
| 04:56
−
| Draw line representing C3 axis of symmetry in a model of '''ethane'''.
+
| Draw line representing '''C3 axis of symmetry''', in a model of '''ethane'''.
  
 
|-
 
|-
 
| 05:02
 
| 05:02
−
| And spin the model along C3 axis.  
+
| And spin the model along '''C3 axis'''.  
  
 
|-
 
|-
Line 261: Line 261:
 
| 05:12
 
| 05:12
 
|  To do so, first delete the lines on the '''methane''' model by typing the following command.  
 
|  To do so, first delete the lines on the '''methane''' model by typing the following command.  
−
 
+
'''draw off ''' (draw space off). Press '''Enter'''.
−
'''draw off ''' (draw space off). Press enter
+
  
 
|-
 
|-
Line 274: Line 273:
 
|-
 
|-
 
| 05:35
 
| 05:35
−
| Number 300 in the command indicates the size of the plane. Press enter.
+
| Number 300 in the command indicates the size of the plane. Press '''Enter'''.
  
 
|-
 
|-
Line 282: Line 281:
 
|-
 
|-
 
| 05:49
 
| 05:49
−
|  To draw a second reflection plane through atoms, 1, 4 and 5:
+
|  To draw a second reflection plane through atoms 1, 4 and 5:
  
 
|-
 
|-
 
| 05:55
 
| 05:55
−
|  In the console press up arrow key and edit the command as follows:
+
|  In the console press up-arrow key and '''edit''' the command as follows:
  
 
|-
 
|-
 
| 06:01
 
| 06:01
−
| Edit '''plane1''' to '''plane2''', and '''atomno2''' to 4 and '''atomno3''' to 5.
+
| Edit '''plane1''' to '''plane2''' and '''atomno2''' to 4 and '''atomno3''' to 5.
  
 
|-
 
|-
 
| 06:12
 
| 06:12
−
|  Also to change the color of the plane type the following command.
+
|  Also to change the color of the plane, type the following command.
  
 
|-
 
|-
 
| 06:17
 
| 06:17
−
| ''';color  $plane2 blue'''(semicolon color space dollar plane2 space blue). Press enter.
+
| ''';color  $plane2 blue'''(semicolon color space dollar plane2 space blue). Press '''Enter'''.
  
 
|-
 
|-
 
| 06:24
 
| 06:24
−
|  On the panel we see the two reflection planes in the '''methane''' molecule.
+
|  On the panel, we see the two reflection planes in the '''methane''' molecule.
  
 
|-
 
|-
Line 310: Line 309:
 
|-
 
|-
 
| 06:36
 
| 06:36
−
| Lets clear the planes drawn on methane molecule on the panel.
+
| Let's clear the planes drawn on methane molecule on the panel.
  
 
|-
 
|-
 
| 06:41
 
| 06:41
−
|  In the console type,  '''draw off ''' (draw space off). Press enter
+
|  In the console, type: '''draw off ''' (draw space off). Press '''Enter'''.
  
 
|-
 
|-
Line 322: Line 321:
 
|-
 
|-
 
| 06:54
 
| 06:54
−
| '''draw pointgroup ''' '''(draw space pointgroup)'''. Press enter.
+
| '''draw pointgroup ''' '''(draw space pointgroup)'''. Press '''Enter'''.
  
 
|-
 
|-
Line 331: Line 330:
 
| 07:04
 
| 07:04
 
|  To find out the point group classification for '''methane''', type the following command.
 
|  To find out the point group classification for '''methane''', type the following command.
−
'''calculate pointgroup'''  (calculate space pointgroup). Press enter
+
'''calculate pointgroup'''  (calculate space pointgroup). Press Enter.
  
 
|-
 
|-
 
| 07:14
 
| 07:14
−
|  '''Td''' the point group of methane molecule, is displayed on the console.
+
|  '''Td''', the point group of methane molecule, is displayed on the console.
  
 
|-
 
|-
Line 343: Line 342:
 
|-
 
|-
 
| 07:25
 
| 07:25
−
| We can draw the structure of allene on the panel using the modelkit menu. Or We can also download the structure of''' allene''' from chemical structure database.  
+
| We can draw the structure of allene on the panel using the '''modelkit''' menu. Or we can also download the structure of''' allene''' from '''chemical structure database'''.  
  
 
|-
 
|-
 
| 07:37
 
| 07:37
−
| If you are connected to internet , click on the '''File''' menu scroll down to '''Get Mol ''' and type '''“allene”''' in the text box . Click on '''OK'''.
+
| If you are connected to internet, click on the '''File''' menu, scroll down to '''Get Mol ''' and type: '''“allene”''' in the text box. Click on '''OK'''.
 
|-
 
|-
 
| 07:48
 
| 07:48
Line 354: Line 353:
 
|-
 
|-
 
| 07:52
 
| 07:52
−
| Press up arrow key at the dollar prompt on the console till you get this command.
+
| Press up-arrow key at the dollar prompt on the console till you get this command.
  
 
|-
 
|-
 
| 07:59
 
| 07:59
−
| '''draw pointgroup '''. Press enter
+
| '''draw pointgroup '''. Press '''Enter'''.
  
 
|-
 
|-
 
| 08:02
 
| 08:02
−
|  Observe the panel, we see all possible symmetry elements for allene.
+
|  Observe the panel, we see all possible symmetry elements for 'allene'.
  
 
|-
 
|-
 
| 08:09
 
| 08:09
−
|  To get the point group classification for allene.
+
|  To get the point group classification for allene-
  
 
|-
 
|-
 
| 08:12
 
| 08:12
−
| Again on the console press up arrow key till you get the command '''calculate pointgroup''' .Press enter
+
| Again on the console press up-arrow key till you get the command '''calculate pointgroup'''. Press '''Enter'''.
  
 
|-
 
|-
 
| 08:21
 
| 08:21
−
|  The point group classification for '''allene''', that is '''D2d '''is displayed on the '''Console.'''
+
|  The point group classification for '''allene''', that is '''D2d, '''is displayed on the '''Console.'''
  
 
|-
 
|-
Line 382: Line 381:
 
|-
 
|-
 
| 08:34
 
| 08:34
−
|  Let's summarize, in this tutorial we learnt   
+
|  Let's summarize. In this tutorial, we learnt:  
  
 
|-
 
|-
 
| 08:38
 
| 08:38
−
| To Draw lines that is C2 and C3 rotational axes through atoms in '''methane''' molecule.
+
|* To Draw lines that is C2 and C3 rotational axes through atoms in '''methane''' molecule.
  
 
|-
 
|-
 
| 08:45
 
| 08:45
−
| Spin and rotate the molecule along the axis.
+
|* Spin and rotate the molecule along the axis.
  
 
|-
 
|-
 
| 08:49
 
| 08:49
−
| Draw reflection plane through atoms in '''methane''' molecule.
+
|* Draw reflection plane through atoms in '''methane''' molecule.
  
 
|-
 
|-
 
| 08:54
 
| 08:54
−
| And demonstrate point group classification using examples of '''methane '''and''' allene.'''
+
|* And demonstrate point group classification using examples of '''methane '''and''' allene.'''
  
 
|-
 
|-
 
| 09:01
 
| 09:01
−
|  As an assignment,
+
|  As an assignment-
  
 
|-
 
|-
Line 418: Line 417:
 
|-
 
|-
 
| 09:15
 
| 09:15
−
| 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.
  
 
|-
 
|-
 
| 09:20
 
| 09:20
−
|  We Conduct workshops using spoken tutorials and give certificates. Please contact us.
+
|  We conduct workshops using spoken tutorials and give certificates. Please contact us.
  
 
|-
 
|-
 
| 09:27
 
| 09:27
−
|  The spoken-tutorial project is funded by NMEICT, MHRD govt of India.
+
|  The spoken-tutorial project is funded by NMEICT, MHRD, govt of India.
  
 
|-
 
|-
 
| 09:33
 
| 09:33
−
|  This is Snehalatha from IIT Bombay signing off.  
+
|  This is Snehalatha from '''IIT Bombay''', signing off.  
−
 
+
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Revision as of 17:48, 14 September 2015

Time
Narration
00:01 Welcome to this tutorial on Symmetry and Point Group in Jmol.
00:06 In this tutorial, we will learn to:
00:08 * Draw line, that is, axis through atoms in a molecule.
00:12 * Spin and rotate the molecule along the axis.
00:17 * Draw plane through atoms in a molecule.
00:21 * And demonstrate point group classification.
00:25 To follow this tutorial, you should have Knowledge of undergraduate Chemistry and familiar with operations from Jmol window.
00:35 If not, for relevant tutorials, please visit our website.
00:39 To record this tutorial, I am using:
00:42 * Ubuntu Operating System version 14.04
00:46 * Jmol version 12.2.32
00:50 * Java version 7 and * Mozilla Firefox browser 35.0
00:57 Often, symmetry in molecules is described in terms of symmetry elements like:
01:03 * Axis of symmetry
01:05 * Plane of symmetry
01:06 * Center of symmetry etc.
01:09 We will use Jmol to display these symmetry elements in a molecule.
01:14 Let us begin this tutorial by drawing C3 rotational axis through atoms in a model of methane.
01:22 I have already opened the Jmol window.
01:25 Click on modelkit menu to get the ball and stick model of methane on the panel.
01:31 Label the atoms in the methane molecule by using Display menu in the tool bar.
01:37 Click on Display, scroll down to Label and click on Number option.
01:43 All the atoms in the methane molecule are now numbered.
01:47 We need to write commands in the console to draw lines and planes through atoms.
01:53 To open the Console, click on File menu.
01:57 Scroll down to Console and click on it.
02:01 Console window opens on the screen.
02:04 We will use draw keyword in the command line to draw lines and planes.
02:10 Detailed information on Jmol script commands is available at this website.
02:15 Open the website in any web browser.
02:19 A web-page opens with a list of keywords used for writing script commands in Jmol.
02:26 Scroll down and click on word draw in the list.
02:31 A page opens with details about the draw keyword.
02:36 A general syntax for the draw command is given at the top of the page.
02:42 This is followed by information regarding the use of the keyword.
02:47 Let us now go back to the Jmol panel.
02:51 I am using Kmag screen magnifier to magnify the console window.
02:55 To draw a line that represents C3 rotational axis:
02:59 Type the following command at the dollar prompt in the console.
03:04 The command line begins with the word “draw”, followed by object ID.
03:10 Number 250 in the command line refers to the length of the line.
03:15 This is followed by the position of the line;
03:18 Within brackets atom number equal to 1 and atom number equal to 2. Press Enter.
03:26 Observe the panel.
03:27 A line passing through atoms 1 and 2 is drawn on the model of methane.
03:33 This line can now act as an axis for rotation.
03:37 We can draw more than one line on a given model.
03:41 To draw C2 rotational axis: Type the following command in the console.
03:47 In this command, the numbers in curly brackets indicate the Cartesian coordinates for the line
03:54 followed by a command to specify the color of the line. Press Enter.
03:59 Now, on the panel, we have methane with C2 and C3 rotational axes.
04:05 To rotate along the line 1, that is C3 axis, type the following command.
04:12 rotate $line1 60 (rotate space dollar line1 space 60).
04:18 The number 60 refers to the degrees of rotation. Press Enter.
04:24 Observe the rotation along line1.
04:27 To spin the molecule along line1, type the following command.
04:32 spin $line1 180 60 (spin space dollar line1 space 180 space 60).
04:39 The number 180 refers to degrees of rotation and 60 refers to the speed of rotation. Press Enter.
04:48 On panel, we see the methane model spin along line1, that is C3 axis.
04:55 As an assignment-
04:56 Draw line representing C3 axis of symmetry, in a model of ethane.
05:02 And spin the model along C3 axis.
05:06 Back to the Jmol panel.
05:08 We can also draw planes going through a set of atoms in a molecule.
05:12 To do so, first delete the lines on the methane model by typing the following command.

draw off (draw space off). Press Enter.

05:24 To draw reflection plane going through atoms 1, 2 and 3 of the methane molecule:
05:31 Type the following command in the console.
05:35 Number 300 in the command indicates the size of the plane. Press Enter.
05:41 Observe the reflection plane going through atoms 1, 2 and 3 in the methane molecule.
05:49 To draw a second reflection plane through atoms 1, 4 and 5:
05:55 In the console press up-arrow key and edit the command as follows:
06:01 Edit plane1 to plane2 and atomno2 to 4 and atomno3 to 5.
06:12 Also to change the color of the plane, type the following command.
06:17 ;color $plane2 blue(semicolon color space dollar plane2 space blue). Press Enter.
06:24 On the panel, we see the two reflection planes in the methane molecule.
06:29 Using Jmol we can also show point group classification for methane as follows.
06:36 Let's clear the planes drawn on methane molecule on the panel.
06:41 In the console, type: draw off (draw space off). Press Enter.
06:47 To display all the possible symmetry elements for methane: Type the following command in the console.
06:54 draw pointgroup (draw space pointgroup). Press Enter.
05:59 We see the symmetry elements of methane displayed on the panel.
07:04 To find out the point group classification for methane, type the following command.

calculate pointgroup (calculate space pointgroup). Press Enter.

07:14 Td, the point group of methane molecule, is displayed on the console.
07:20 Another classic example for point group demonstration is allene.
07:25 We can draw the structure of allene on the panel using the modelkit menu. Or we can also download the structure of allene from chemical structure database.
07:37 If you are connected to internet, click on the File menu, scroll down to Get Mol and type: “allene” in the text box. Click on OK.
07:48 To display all possible symmetry elements for allene:
07:52 Press up-arrow key at the dollar prompt on the console till you get this command.
07:59 draw pointgroup . Press Enter.
08:02 Observe the panel, we see all possible symmetry elements for 'allene'.
08:09 To get the point group classification for allene-
08:12 Again on the console press up-arrow key till you get the command calculate pointgroup. Press Enter.
08:21 The point group classification for allene, that is D2d, is displayed on the Console.
08:28 Similarly you can download molecules of your choice and calculate their point group.
08:34 Let's summarize. In this tutorial, we learnt:
08:38 * To Draw lines that is C2 and C3 rotational axes through atoms in methane molecule.
08:45 * Spin and rotate the molecule along the axis.
08:49 * Draw reflection plane through atoms in methane molecule.
08:54 * And demonstrate point group classification using examples of methane and allene.
09:01 As an assignment-
09:02 Draw reflection plane in a model of dichloromethane.
09:07 And find out the point group classification for ammonia and benzene.
09:12 This video summarizes the Spoken Tutorial project.
09:15 If you do not have good bandwidth, you can download and watch it.
09:20 We conduct workshops using spoken tutorials and give certificates. Please contact us.
09:27 The spoken-tutorial project is funded by NMEICT, MHRD, govt of India.
09:33 This is Snehalatha from IIT Bombay, signing off.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Jmol-Application/C4/Symmetry-and-Point-Groups/English-timed&oldid=23599"