Avogadro/C3/General-Features-in-Avogadro/English-timed - Revision history

Sandhya.np14 at 15:14, 13 July 2018

2018-07-13T15:14:53Z

Sandhya.np14 at 12:25, 5 June 2018

2018-06-05T12:25:53Z

Sandhya.np14 at 12:11, 5 June 2018

2018-06-05T12:11:13Z

PoojaMoolya: Created page with "{|border=1 |'''Time''' |'''Narration''' |- |00:01 |Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- |00:08 |In this tutorial we will learn..."

2017-09-02T06:27:39Z

Created page with "{|border=1 |'''Time''' |'''Narration''' |- |00:01 |Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''. |- |00:08 |In this tutorial we will learn..."

New page

{|border=1
|'''Time'''
|'''Narration'''

|-
|00:01
|Warm greetings! Welcome to this tutorial on '''General Features in Avogadro'''.

|-
|00:08
|In this tutorial we will learn about: '''Proton transfer''' in compounds by changing '''pH values'''

|-
|00:16
| Load crystal structures

|-
| 00:19
| Show various '''Miller planes'''

|-
|00:22
|Build super cells

|-
|00:24
| Show geometries in coordination compounds and Build '''nanotubes'''

|-
|00:31
|Here I am using, '''Ubuntu Linux''' OS version 14.04

|-
|00:37
|'''Avogadro''' version 1.1.1.

|-
|00:41
|To follow this tutorial, you should be familiar with, '''Avogadro''' interface.

|-
|00:47
|If not, for relevant tutorials, please visit our website.

|-
|00:52
|Example files used in this tutorial are provided as code files.

|-
|00:58
|I have opened a new '''Avogadro''' window.

|-
|01:01
|I will demonstrate '''proton transfer''' in compounds by changing '''pH values'''.

|-
|01:07
|For this, I will load '''amino acids''' from '''Fragment library'''.

|-
|01:12
|Using '''Build''' menu, go to '''Fragment library'''.

|-
|01:16
|In the '''Fragment library,''' double click on '''Amino acids''' folder.

|-
|01:21
|Select '''D-alanine.cml''' and click on '''Insert'''.

|-
|01:26
|Close '''Insert Fragment''' dialog box.

|-
|01:30
|Press '''CTRL, SHIFT''' and '''A''' to deselect the structure.

|-
|01:34
|Using '''Navigation''' tool rotate the structure for proper orientation.

|-
|01:39
|I will demonstrate '''proton transfer''' in '''amino acids''' by changing '''pH'''.

|-
|01:46
|Go to '''Build''' menu and select '''Add Hydrogens for pH'''.

|-
|01:51
|'''Add Hydrogens for pH''' text box opens with default value 7.4.

|-
|01:57
|In the text box change '''pH value''' to 7.0.Click '''OK'''.

|-
|02:04
|Notice the structure. '''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''

|-
|02:11
|'''Amino group(NH2)''' gets '''protonated(NH3+)'''.

|-
|02:15
|Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.

|-
|02:20
|In the text box, change '''pH''' to 2.0 and click '''Ok'''.

|-
|02:26
|'''Carboxylate ion''' has been converted to '''Carboxylic group'''.

|-
|02:31
|Go to '''Build''' menu and select '''Add Hydrogens for pH'''.

|-
|02:35
|In the text box, change '''pH''' to 10.0 and click '''Ok'''.

|-
|02:41
|'''Carboxylic group''' has been converted to '''Carboxylate ion'''.

|-
|02:46
|'''Amino''' group(NH2) is '''deprotonated'''.

|-
|02:49
|Press '''Delete''' key to delete the structure.

|-
|02:52
|Now, I will demonstrate '''proton transfer''' in '''amines''' by changing '''pH'''.

|-
|02:58
|For this I will load '''ethylamine''' structure from '''Fragment library'''.

|-
|03:05
|Close '''Insert Fragment''' dialog box.

|-
|03:09
|Press '''CTRL, SHIFT''' and '''A''' to deselect the structure.

|-
|03:13
|Using '''Navigation ''' tool, rotate the structure for proper orientation.

|-
|03:18
|Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.

|-
|03:23
|'''Add Hydrogens for pH''' text box opens.

|-
|03:27
|In the text box, change '''pH''' value to 7.0. Click on '''OK'''.

|-
|03:34
|Observe the structure. '''Amino''' group is '''protonated'''.

|-
|03:39
|Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.

|-
|03:43
|In the text box, change '''pH''' to 2.0 and click '''OK'''.

|-
|03:49
|Here we see no change in the structure.

|-
|03:53
|As '''ethylamine''' shows '''proton transfer''' in basic medium only.

|-
|03:59
|Go to '''Build''' menu, click on '''Add Hydrogens for pH'''.

|-
|04:03
|In the text box, change '''pH''' to 10.0 and click '''OK'''.

|-
|04:09
|'''Amino group''' gets '''deprotonated'''.

|-
|04:12
|Now I will demonstrate: how to load '''Crystal structures''' from '''Crystal Library''' and some '''Crystal properties'''.

|-
|04:20
|Click on '''New''' icon on the tool bar, to open a new window.

|-
|04:25
|Go to '''File''' menu, navigate to '''Import''' and select '''Crystal'''.

|-
|04:30
|'''Insert Crystal''' dialog box opens.

|-
|04:34
|Here we can see different folders.

|-
|04:37
|Double-click on '''halides''' folder.

|-
|04:40
|Select '''NaCl-Halite.cif''' file and click on '''Insert'''.

|-
|04:47
|Close '''Insert Crystal''' dialog box.

|-
|04:51
|Here I will close '''Tool Settings''' and '''Display Settings''' for proper view.

|-
|04:58
|'''Crystal''' structure of '''sodium chloride''' is displayed on the '''Panel'''.

|-
|05:02
|Along with the structure, its '''Cell Parameters''' are displayed.

|-
|05:07
|On the top-left side of the '''Panel''' you can see:

'''Lattice Type'''

'''Spacegroup''' and

'''Unit cell volume''' of '''sodium chloride crystal'''.

|-
|05:18
|Now I will show '''Miller planes''' for this '''crystal'''.

|-
|05:22
|Before that I will give a brief introduction about '''Miller indices'''.

|-
|05:28
|'''Miller Indices''' are a set of three numbers ('''hkl''').

|-
|05:34
|They are used to specify directions and internal '''planes''' in '''crystal systems'''.

|-
|05:41
|Now to '''Miller planes''' in '''sodium chloride crystal'''.

|-
|05:45
|Go to '''View''' menu and click on '''Crystal View Options'''.

|-
|05:51
|'''Crystal View Options''' menu, gets loaded on the right.

|-
|05:56
|Click on '''Miller Indices''' radio button.

|-
|06:00
|I will change the values of ''''h', 'k', 'l'''' to 2, 3, 2.

|-
|06:07
|Notice the change in '''planes''' and position of '''atoms''' in the '''crystal'''.

|-
|06:13
|Now I will explain how to build a super cell.

|-
|06:17
|Go to '''Build''' menu and select '''Super Cell Builder'''.

|-
|06:22
|'''Super Cell Parameters''' dialog box opens.

|-
| 06:26
|Under '''Super Cell Options,''' we can change '''unit cell parameters 'A', 'B'''' and ''''C''''.

|-
|06:34
|I will change the field values of ''''A', 'B'''' and ''''C'''' to '2', '2', '2'.

|-
|06:43
|Then click on '''Generate cell'''. Click on '''Close''' to close the dialog box.

|-
|06:50
|Zoom the structure as required for proper view.

|-
|06:55
|'''Crystal lattice''' is displayed on the Panel.

|-
|06:59
|Now I will change '''Miller Indices''' to 3, 2, 3.

|-
|07:05
|Rotate the cell using '''Navigation''' tool.

|-
|07:09
|Here dotted figure shows the '''plane'''.

|-
|07:13
|You can see various '''planes''' by changing ''''h', 'k', 'l'''' values.

|-
|07:20
|Now I will build '''octahedral''' geometry for '''Hexamminecobalt(III)'''.

|-
|07:26
|Click on '''New''' icon on the tool bar to open a new window.

|-
|07:31
|To draw '''Hexammine cobalt(III)''', click on '''Draw''' tool icon.

|-
|07:37
|In the '''Element''' drop down select '''Other'''.

|-
|07:41
|'''Periodic table''' window opens.

|-
|07:44
|Select '''Cobalt''' from the table.

|-
|07:47
|Close '''Periodic table''' window.

|-
|07:50
|Click on the '''Panel'''. Select '''Nitrogen''' from '''Element''' drop down.

|-
|07:56
|Click and drag to draw six '''bonds''' on '''cobalt atom'''.

|-
|08:03
|Notice that each '''Nitrogen''' has two attached '''hydrogens'''.

|-
|08:08
|In '''hexamminecobalt(III)''' structure, each '''nitrogen''' has three attached '''hydrogens'''.

|-
|08:15
|Select '''Hydrogen''' from '''Element''' drop down.

|-
|08:19
|Click and drag on all '''Nitrogen atoms'''.

|-
|08:25
|'''Hexamminecobalt(III)''' structure is drawn on the Panel.

|-
|08:29
|Click on '''Display Settings''' button to open '''Display Settings''' menu.

|-
|08:36
|Now I will show '''octahedral geometry''' of '''Hexamminecobalt(III)''' structure.

|-
|08:42
|For this, I will use '''Polygon Display Type'''.

|-
|08:46
|If '''Polygon Display Type''' is not activated, use '''Add''' button to activate.

|-
|08:52
|Click on '''Polygon Display Type''' checkbox.

|-
|08:56
|To optimize, click on '''Auto Optimization Tool''' on the tool bar.

|-
|09:01
|In the '''Force Field''' drop down, select '''UFF'''.

|-
|09:06
|Click on '''Start''' button to optimize.

|-
|09:11
|Click on '''Stop''' to stop the '''Auto optimization''' process.

|-
|09:16
|Using '''Navigation''' tool, rotate the structure to see '''octahedral geometry'''.

|-
|09:22
|Similarly, this is '''pentagonal bipyramidal geometry''' of '''iodine heptafluoride'''.

|-
|09:29
|Now we will see another feature in '''Build''' menu called '''Nanotube builder'''.

|-
|09:35
|A '''nanotube''' is a '''nanometer-scale tube'''-like structure.

|-
|09:40
|Examples of different types of '''nanotubes''' are: '''Boron carbon nitrogen''', '''Boron carbon''' and '''Carbon'''.

|-
|09:50
|A '''carbon nanotube''', is a miniature cylindrical '''carbon structure''' that has hexagonal '''graphite molecules''' attached at the edges.
|-
|10:01
|Click on '''New''' icon on the tool bar to open a new window.

|-
|10:06
|For a better view of the '''nanotube''', I will change background color to blue.

|-
|10:12
|Go to '''View''' and navigate to '''Set Background Color'''.

|-
|10:17
|'''Select Color''' dialog box opens.

|-
|10:21
|In the box, select blue colour and click '''Ok'''.

|-
|10:26
|Go to '''Build''' menu and select '''Nanotube Builder.'''

|-
|10:30
|'''Nanotube Builder''' menu opens below the '''Panel'''.

|-
|10:35
|I will re-size '''Avogadro''' window to view '''Nanotube Builder''' menu.

|-
|10:40
|You can set '''chirality indexes n, m''' to determine the type of '''nanotube'''.

|-
|10:47
|I will set '''index values n''' and '''m''' to 4 and 4.

|-
|10:53
|Change '''Length''' to 4.00(four point zero and zero).

|-
|10:57
|Set '''Unit '''field to '''Periodic units'''.

|-
|11:01
|Click on '''Find double bonds''' checkbox to show double bonds in the '''nanotube'''.

|-
|11:08
|Then click on '''Build'''.

|-
|11:10
|Press '''CTRL + SHIFT + A''' to deselect the structure.

|-
|11:15
|Using '''Navigation''' tool rotate and zoom the '''nanotube''' for proper view.

|-
|11:21
|Next I will build a nanotube with 6,6 '''index values'''.

|-
|11:27
|Go to '''Build''' menu and select '''Nanotube Builder'''.

|-
|11:31
|Change '''n '''and '''m''' values to 6 and 6. Then click on '''Build'''.

|-
|11:40
|Notice the two overlapping '''nanotubes'''.

|-
|11:44
|To optimize the '''nanotubes''', click on '''Auto Optimization Tool'''.

|-
|11:50
|In the '''Force Field''' drop down, select '''MMFF94'''.

|-
|11:56
|Click on '''Start''' button to optimize.

|-
|12:02
|Click on '''Stop''' to stop the '''auto optimization''' process.

|-
|12:07
|Press '''CTRL + SHIFT + A''' to deselect the structure.

|-
|12:11
|A double-walled '''nanotube''' is displayed on the '''Panel'''.

|-
|12:16
|Using '''Navigation tool,''' rotate the '''nanotube''' for proper view.

|-
| 12:21
| Now I will show '''carbon hexagon rings''' in the '''nanotube'''.

|-
|12:26
|In the '''Display Types''' menu, select ''' Ring''' checkbox.

|-
|12:31
|Using '''Navigation''' tool rotate the '''nanotube''' to see '''carbon hexagons'''.

|-
|12:38
|Let's summarize.

|-
|12:40
|In this tutorial we have learnt about:

|-
|12:43
| '''Proton transfer''' in compounds by changing '''pH values'''

|-
|12:48
| Load '''crystal structures''' from '''crystal library'''

|-
|12:51
|Show various '''Miller planes'''

|-
|12:54
| Build super cells

|-
|12:56
| Show geometries in coordination compounds and Build '''nanotubes'''

|-
|13:03
|As an assignment

Load '''silver chloride(AgCl) crystal structure''' and its show '''Miller planes'''.

|-
|13:09
|Load structures from coordination library and show geometries.

|-
|13:14
|Build '''nanotube''' with '''chirality index''' 9,9.

|-
|13:19
|This video summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.

|-
|13:27
| We conduct workshops using Spoken Tutorials and give certificates. Please contact us.

|-
|13:34
|The Spoken Tutorial Project is funded by '''NMEICT, MHRD Government of India'''.

|-
|13:41
|This is Madhuri Ganapathi singing off. Thank you for joining.
|-
|}

@@ Line 612: / Line 612: @@
 |As an assignment:
-Load '''silver chloride(AgCl) crystal structure''' and its show '''Miller planes'''.
+Load '''silver chloride(AgCl) crystal structure''' and show its '''Miller planes'''.
 |-

@@ Line 133: / Line 133: @@
 |-
 |02:46
-|'''Amino''' group(NH2) is '''deprotonated'''.
+|'''Amino''' group(NH2) is deprotonated.
 |-
@@ Line 141: / Line 141: @@
 |-
 |02:52
-|Now, I will demonstrate '''proton transfer''' in '''amines''' by changing '''pH'''.
+|Now, I will demonstrate proton transfer in '''amines''' by changing '''pH'''.
 |-
 |02:58
-|For this I will load '''ethylamine''' structure from '''Fragment library'''.
+|For this, I will load '''ethylamine''' structure from '''Fragment library'''.
 |-
@@ Line 173: / Line 173: @@
 |-
 |03:34
-|Observe the structure. '''Amino''' group is '''protonated'''.
+|Observe the structure. '''Amino''' group is protonated.
 |-
@@ Line 201: / Line 201: @@
 |-
 |04:09
-|'''Amino group''' gets '''deprotonated'''.
+|'''Amino group''' gets deprotonated.
 |-
 |04:12
-|Now I will demonstrate:  how to load '''Crystal structures''' from '''Crystal Library''' and some '''Crystal properties'''.
+|Now I will demonstrate how to load '''Crystal structures''' from '''Crystal Library''' and some '''Crystal properties'''.
 |-
 |04:20
-|Click on '''New''' icon on the tool bar, to open a new window.
+|Click on '''New''' icon on the tool bar to open a new window.
 |-
@@ Line 237: / Line 237: @@
 |-
 |04:51
-|Here I will close '''Tool Settings''' and '''Display Settings''' for proper view.
+|Here, I will close '''Tool Settings''' and '''Display Settings''' for proper view.
 |-
@@ Line 263: / Line 263: @@
 |-
 |05:22
-|Before that I will give a brief introduction about '''Miller indices'''.
+|Before that, I will give a brief introduction about '''Miller indices'''.
 |-
@@ Line 283: / Line 283: @@
 |-
 |05:51
-|'''Crystal View Options''' menu, gets loaded on the right.
+|'''Crystal View Options''' menu gets loaded on the right.
 |-
@@ Line 295: / Line 295: @@
 |-
 |06:07
-|Notice the change in '''planes''' and position of '''atoms''' in the '''crystal'''.
+|Notice the change in '''planes''' and position of atoms in the crystal.
 |-
@@ Line 339: / Line 339: @@
 |-
 |07:09
-|Here dotted figure shows the '''plane'''.
+|Here, dotted figure shows the '''plane'''.
 |-
 |07:13
-|You can see various '''planes''' by changing ''''h', 'k', 'l'''' values.
+|You can see various planes by changing ''''h', 'k', 'l'''' values.
 |-
 |07:20
-|Now I will build '''octahedral''' geometry for '''Hexamminecobalt(III)'''.
+|Now, I will build '''octahedral''' geometry for '''Hexamminecobalt(III)'''.
 |-
@@ Line 359: / Line 359: @@
 |-
 |07:37
-|In the '''Element''' drop down select '''Other'''.
+|In the '''Element''' drop down, select '''Other'''.
 |-
@@ Line 395: / Line 395: @@
 |-
 |08:19
-|Click and drag on all '''Nitrogen atoms'''.
+|Click and drag on all Nitrogen atoms.
 |-
@@ Line 407: / Line 407: @@
 |-
 |08:36
-|Now I will show '''octahedral geometry''' of '''Hexamminecobalt(III)''' structure.
+|Now, I will show '''octahedral geometry''' of '''Hexamminecobalt(III)''' structure.
 |-
@@ Line 459: / Line 459: @@
 |-
 |09:50
-|A '''carbon nanotube''', is a miniature cylindrical '''carbon structure''' that has hexagonal '''graphite molecules''' attached at the edges.
+|A '''carbon nanotube''' is a miniature cylindrical '''carbon structure''' that has hexagonal '''graphite molecules''' attached at the edges.
 |-
 |10:01
@@ Line 502: / Line 502: @@
 |-
 |10:53
-|Change '''Length''' to 4.00(four point zero and zero).
+|Change '''Length''' to 4.00 (four point zero and zero).
 |-
@@ Line 522: / Line 522: @@
 |-
 |11:15
-|Using '''Navigation''' tool rotate and zoom the '''nanotube''' for proper view.
+|Using '''Navigation''' tool, rotate and zoom the '''nanotube''' for proper view.
 |-
@@ Line 586: / Line 586: @@
 |-
 |12:40
-|In this tutorial we have learnt about:
+|In this tutorial, we have learnt about:
 |-
 |12:43
-| '''Proton transfer''' in compounds by changing '''pH values'''
+| '''Proton transfer''' in compounds by changing '''pH values''',
 |-
 |12:48
-| Load '''crystal structures''' from '''crystal library'''
+| load '''crystal structures''' from '''crystal library''',
 |-
 |12:51
-|Show various '''Miller planes'''
+|show various '''Miller planes''',
 |-
 |12:54
-| Build super cells
+| build super cells,
 |-
 |12:56
-| Show geometries in coordination compounds and  Build '''nanotubes'''
+| show geometries in coordination compounds and  Build '''nanotubes'''.
 |-
 |13:03
-|As an assignment
+|As an assignment:
 Load '''silver chloride(AgCl) crystal structure''' and its show '''Miller planes'''.
@@ Line 624: / Line 624: @@
 |-
 |13:19
-|This video summarises the Spoken Tutorial project.  If you do not have good bandwidth, you can download and watch it.
+|This video summarizes the '''Spoken Tutorial''' project.  If you do not have good bandwidth, you can download and watch it.
 |-

@@ Line 9: / Line 9: @@
 |-
 |00:08
-|In this tutorial we will learn about:  '''Proton transfer''' in compounds by changing '''pH values'''
+|In this tutorial, we will learn about:  '''Proton transfer''' in compounds by changing '''pH values''',
 |-
 |00:16
-| Load crystal structures
+| '''load''' crystal structures,
 |-
 | 00:19
-| Show various '''Miller planes'''
+| show various '''Miller planes''',
 |-
 |00:22
-|Build super cells
+|build super cells,
 |-
 |00:24
-| Show geometries in coordination compounds and  Build '''nanotubes'''
+| show geometries in coordination compounds and  Build '''nanotubes'''.
 |-
 |00:31
-|Here I am using, '''Ubuntu Linux''' OS version 14.04
+|Here I am using '''Ubuntu Linux''' OS version 14.04,
 |-
@@ Line 37: / Line 37: @@
 |-
 |00:41
-|To follow this tutorial, you should be familiar with, '''Avogadro''' interface.
+|To follow this tutorial, you should be familiar with '''Avogadro''' interface.
 |-
@@ Line 45: / Line 45: @@
 |-
 |00:52
-|Example files used in this tutorial are provided as code files.
+|Example files used in this tutorial are provided as '''code files'''.
 |-
@@ Line 81: / Line 81: @@
 |-
 |01:34
-|Using '''Navigation''' tool rotate the structure for proper orientation.
+|Using '''Navigation''' tool, rotate the structure for proper orientation.
 |-
@@ Line 97: / Line 97: @@
 |-
 |01:57
-|In the text box change '''pH value''' to 7.0.Click '''OK'''.
+|In the text box, change '''pH value''' to 7.0.Click '''OK'''.
 |-
 |02:04
-|Notice the structure.  '''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''
+|Notice the structure.  '''Carboxylic group(COOH)''' has been converted to '''Carboxylate ion'''.
 |-
@@ Line 109: / Line 109: @@
 |-
 |02:15
-|Go to '''Build ''' menu, and select '''Add Hydrogens for pH'''.
+|Go to '''Build ''' menu and select '''Add Hydrogens for pH'''.
 |-