Difference between revisions of "Avogadro/C2/Edit-molecules/English-timed"

From Script | Spoken-Tutorial
Jump to: navigation, search
(Created page with " {| border=1 ||'''Time''' ||'''Narration''' |- ||00:01 || Warm greetings everyone. Welcome to this tutorial on '''Edit molecules.''' |- || 00:08 || In this tutorial, we wil...")
 
 
(2 intermediate revisions by the same user not shown)
Line 10: Line 10:
 
|-
 
|-
 
|| 00:08
 
|| 00:08
−
|| In this tutorial, we will learn to-  Add and delete atoms
+
|| In this tutorial, we will learn to-  add and delete atoms,
  
 
|-
 
|-
 
|| 00:14
 
|| 00:14
−
||Add and delete bonds
+
||add and delete '''bond'''s,
  
 
|-
 
|-
 
|| 00:16
 
|| 00:16
−
||Rotate bonds  
+
||rotate bonds,
  
 
|-
 
|-
 
|| 00:18
 
|| 00:18
−
||Change length of the bond
+
||change length of the bond,
  
 
|-
 
|-
 
|| 00:20
 
|| 00:20
−
||Change hydrogen to methyl group
+
||change hydrogen to methyl group,
  
 
|-
 
|-
 
|| 00:23
 
|| 00:23
−
||Copy, paste and join structures.
+
||'''copy, paste''' and join structures.
  
 
|-
 
|-
 
||00:27
 
||00:27
−
|| Here I am using
+
|| Here I am using:
  
−
'''Ubuntu Linux''' OS version. 14.04
+
'''Ubuntu Linux''' OS version. 14.04,
  
 
'''Avogadro''' version 1.1.1.
 
'''Avogadro''' version 1.1.1.
Line 54: Line 54:
 
|-
 
|-
 
|| 00:55
 
|| 00:55
−
|| To open the terminal press '''CTRL, ALT''' and '''T '''keys simultaneously.
+
|| To open the '''terminal''', press '''CTRL, ALT''' and '''T '''keys simultaneously.
  
 
|-
 
|-
 
|| 01:03
 
|| 01:03
−
|| Type '''avogadro '''at the prompt and press enter.
+
|| Type '''avogadro '''at the '''prompt''' and press '''Enter'''.
  
 
|-
 
|-
 
|| 01:08
 
|| 01:08
−
||'''Avogadro''' application window opens.
+
||'''Avogadro''' '''application window''' opens.
  
 
|-
 
|-
 
|| 01:12
 
|| 01:12
−
|| For demonstration, I will display a molecule of '''n-butane''' from the '''Fragment''' library.
+
|| For demonstration, I will display a molecule of '''n-butane''' from the '''Fragment''' '''library'''.
  
 
|-
 
|-
Line 78: Line 78:
 
|-
 
|-
 
|| 01:29
 
|| 01:29
−
|| From the list of fragments, double click on '''alkanes''' folder to open.
+
|| From the list of '''fragment'''s, double click on '''alkanes''' folder to open.
  
 
|-
 
|-
Line 90: Line 90:
 
|-
 
|-
 
|| 01:49
 
|| 01:49
−
|| '''Butane''' molecule highlighted in blue color appears on the '''Panel'''.
+
|| '''Butane''' molecule, highlighted in blue color, appears on the '''Panel'''.
  
 
|-
 
|-
Line 106: Line 106:
 
|-
 
|-
 
||  02:14
 
||  02:14
−
|| Click on '''Draw tool''' icon on the tool bar.
+
|| Click on '''Draw tool''' icon on the '''tool bar'''.
  
 
|-
 
|-
Line 122: Line 122:
 
|-
 
|-
 
|| 02:32
 
|| 02:32
−
||Similarly, you can add atoms using '''Draw tool''' to make a series of alkanes.
+
||Similarly, you can add atoms using '''Draw tool''' to make a series of '''alkane'''s.
  
 
|-
 
|-
 
|| 02:39
 
|| 02:39
−
|| Open a new window. Draw propane using '''Draw tool.'''
+
|| Open a new window. Draw '''propane''' using '''Draw tool.'''
  
 
|-
 
|-
Line 142: Line 142:
 
|-
 
|-
 
|| 03:02
 
|| 03:02
−
||Selected atoms appears blue in color.
+
||Selected atoms appear blue in color.
  
 
|-
 
|-
 
|| 03:06
 
|| 03:06
−
|| Press '''Backspace''' to delete. Alternatively you can use clear option in '''Edit''' menu.
+
|| Press '''Backspace''' to delete. Alternatively, you can use clear option in '''Edit''' menu.
  
 
|-
 
|-
 
|| 03:14
 
|| 03:14
−
||To redo, press '''Ctrl and Z keys '''simultaneously.
+
||To '''redo''', press '''Ctrl''' and '''Z''' keys simultaneously.
  
 
|-
 
|-
 
|| 03:20
 
|| 03:20
−
|| We will demonstrate on how to add and delete bonds in a molecule.
+
|| We will demonstrate on how to add and delete '''bond'''s in a molecule.
  
 
|-
 
|-
 
|| 03:26
 
|| 03:26
−
|| To add bonds select the '''Draw tool''' icon on the tool bar.  
+
|| To add bonds, select the '''Draw tool''' icon on the tool bar.  
  
 
|-
 
|-
 
|| 03:31
 
|| 03:31
−
||'''Draw Settings''' menu open on the left.
+
||'''Draw Settings''' menu opens on the left.
  
 
|-
 
|-
 
|| 03:35
 
|| 03:35
−
|| By default '''Carbon''' is selected in the '''Element '''drop down list.
+
|| By default, '''Carbon''' is selected in the '''Element '''drop down list.
  
 
|-
 
|-
 
|| 03:40
 
|| 03:40
−
||To introduce a double bond select '''Double''' from '''Bond Order '''drop down.
+
||To introduce a double bond, select '''Double''' from '''Bond Order '''drop down.
  
 
|-
 
|-
Line 184: Line 184:
 
|-
 
|-
 
|| 03:59
 
|| 03:59
−
|| To delete bonds, hold the right mouse button and click on the bonds.
+
|| To delete bonds, hold the right '''mouse button''' and click on the bonds.
  
 
|-
 
|-
Line 248: Line 248:
 
|-
 
|-
 
|| 05:21
 
|| 05:21
−
|| To change length of the bond hold the right mouse button and drag.
+
|| To change length of the bond, hold the right '''mouse button''' and drag.
  
 
|-
 
|-
Line 260: Line 260:
 
|-
 
|-
 
|| 05:38
 
|| 05:38
−
|| All '''Hydrogens''' are now replaced by '''Methyl''' groups.
+
|| All Hydrogens are now replaced by '''Methyl''' groups.
  
 
|-
 
|-
 
|| 05:43
 
|| 05:43
−
||Press '''CTRL''' and ''' Z keys''' simultaneously to undo the changes.
+
||Press '''CTRL''' and ''' Z''' keys simultaneously to '''undo''' the changes.
  
 
|-
 
|-
 
||05:49
 
||05:49
−
|| We can also select a particular '''hydrogen''' atom and change it to a '''methyl''' group.
+
|| We can also select a particular hydrogen atom and change it to a '''methyl''' group.
  
 
|-
 
|-
Line 276: Line 276:
 
|-
 
|-
 
|| 05:59
 
|| 05:59
−
|| Click on the '''hydrogen''' attached to end carbon atom to select.
+
|| Click on the hydrogen attached to end carbon atom to select.
  
 
|-
 
|-
Line 292: Line 292:
 
|-
 
|-
 
|| 06:22
 
|| 06:22
−
|| Let us take a look as how to copy, paste and join structures.
+
|| Let us take a look as how to '''copy, paste''' and join structures.
  
 
|-
 
|-
 
|| 06:28
 
|| 06:28
−
|| Click on '''File'''-> '''New''' to open a new window.
+
|| Click on '''File'''-> '''New''' to open a new '''window'''.
  
 
|-
 
|-
Line 316: Line 316:
 
|-
 
|-
 
|| 06:51
 
|| 06:51
−
|| '''Insert''' -> '''Fragment''' dialog box appears.
+
|| '''Insert Fragment''' dialog box appears.
  
 
|-
 
|-
Line 336: Line 336:
 
|-
 
|-
 
|| 07:16
 
|| 07:16
−
|| '''beta-D-glucopyranose.cml''' appears on panel highlighted in blue color.
+
|| '''beta-D-glucopyranose.cml''' appears on '''panel''' highlighted in blue color.
  
 
|-
 
|-
 
|| 07:24
 
|| 07:24
−
||Translate it to the center using hand tool.
+
||'''Translate''' it to the center, using hand tool.
  
 
|-
 
|-
 
|| 07:28
 
|| 07:28
−
|| Let us copy and paste another '''glucose''' molecule.
+
|| Let us '''copy''' and '''paste''' another '''glucose''' molecule.
  
 
|-
 
|-
Line 352: Line 352:
 
|-
 
|-
 
|| 07:36
 
|| 07:36
−
|| And click on '''Copy'''.Again Scroll down the edit menu and then click '''Paste'''.
+
|| And click on '''Copy'''. Again scroll down the '''Edit''' menu and then click '''Paste'''.
  
 
|-
 
|-
 
|| 07:44
 
|| 07:44
−
|| Please note during copy, paste operation, window dims for a moment and then recovers.
+
|| Please note: during '''copy, paste''' operation, window dims for a moment and then recovers.
  
 
|-
 
|-
 
|| 07:51
 
|| 07:51
−
|| A new molecule gets copied and pasted on the existing molecule on the Panel.
+
|| A new molecule gets copied and pasted on the existing molecule on the '''panel'''.
  
 
|-
 
|-
Line 372: Line 372:
 
|-
 
|-
 
|| 08:06
 
|| 08:06
−
||Now we have two separate molecules on the Panel
+
||Now we have two separate molecules on the panel.
  
 
|-
 
|-
 
|| 08:10
 
|| 08:10
−
|| To de-select Press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
+
|| To de-select, press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
  
 
|-
 
|-
 
|| 08:17
 
|| 08:17
−
|| Let us label the molecules.Labeling helps to identify the positions of all the atoms.
+
|| Let us label the molecules. Labeling helps to identify the positions of all the atoms.
  
 
|-
 
|-
 
|| 08:25
 
|| 08:25
−
|| To label, Click on '''Label''' check box from the''' Display Types''' drop down.
+
|| To label, click on '''Label''' check-box from the''' Display Types''' drop down.
 
|-
 
|-
 
|| 08:32
 
|| 08:32
−
|| To get '''Maltose''' we need to remove a water molecule.  
+
|| To get '''maltose''', we need to remove a water molecule.  
 
|-
 
|-
 
|| 08:37
 
|| 08:37
−
|| Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
+
|| Delete the '''OH''' group on '''C-1''' of first molecule and hydrogen on '''C-9''' of second molecule.
  
 
|-
 
|-
Line 406: Line 406:
 
|-
 
|-
 
|| 08:58
 
|| 08:58
−
|| Click and drag to join C-1 of first molecule and C-9 of second molecule through '''oxygen''' atom.
+
|| Click and drag to join '''C-1''' of first molecule and '''C-9''' of second molecule through '''oxygen''' atom.
  
 
|-
 
|-
Line 426: Line 426:
 
|-
 
|-
 
|| 09:27
 
|| 09:27
−
|| The optimization may take a few seconds to complete. You may remove the labels now
+
|| The optimization may take a few seconds to complete. You may remove the labels now.
  
 
|-
 
|-
 
|| 09:35
 
|| 09:35
−
|| We now have an optimized structure of '''Maltose''' on Panel.
+
|| We now have an optimized structure of '''maltose''' on panel.
  
 
|-
 
|-
 
|| 09:40
 
|| 09:40
−
|| Let's summarize. In this tutorial we have learnt to: Add and delete atoms
+
|| Let's summarize. In this tutorial, we have learnt to: add and delete atoms,
  
 
|-
 
|-
 
|| 09:47
 
|| 09:47
−
||Add and delete bonds
+
||add and delete '''bond'''s,
  
 
|-
 
|-
 
|| 09:50
 
|| 09:50
−
||Rotate bonds  
+
||rotate bonds,
  
 
|-
 
|-
 
|| 09:52
 
|| 09:52
−
||Change Bond length
+
||change bond length,
  
 
|-
 
|-
 
|| 09:54
 
|| 09:54
−
||Change Hydrogen to Methyl group
+
||change hydrogen to methyl group,
  
 
|-
 
|-
 
|| 09:56
 
|| 09:56
−
||Copy, paste and join structures.
+
||copy, paste and join structures.
  
 
|-
 
|-
 
|| 10:00
 
|| 10:00
−
|| As an assignment, Create a Butane molecule using draw tool
+
|| As an assignment, create a '''Butane''' molecule using '''draw''' tool.
  
 
|-
 
|-
 
|| 10:06
 
|| 10:06
−
||Convert it into '''2,3 dimethyl Butane'''
+
||Convert it into '''2,3 dimethyl Butane'''.
  
 
|-
 
|-
Line 470: Line 470:
 
|-
 
|-
 
|| 10:14
 
|| 10:14
−
||Create a molecule of '''cellulose'''  (Hint: D- glucose monomer is available in the Insert fragment library)
+
||Create a molecule of '''cellulose'''  (Hint: D- glucose monomer is available in the '''Insert fragment''' library)
  
 
|-
 
|-
 
|| 10:22
 
|| 10:22
−
||Optimize the geometry using UFF force field.
+
||Optimize the geometry using '''UFF force field'''.
  
 
|-
 
|-
 
|| 10:27
 
|| 10:27
−
|| This video summarises the Spoken Tutorial project, If you do not have good bandwidth, you can download and watch it.
+
|| This video summarises the '''Spoken Tutorial''' project. If you do not have good '''bandwidth''', you can download and watch it.
  
 
|-
 
|-
Line 486: Line 486:
 
|-
 
|-
 
||  10:44
 
||  10:44
−
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India
+
|| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.
 
|-
 
|-
 
|| 10:52
 
|| 10:52

Latest revision as of 21:46, 6 July 2018

Time Narration
00:01 Warm greetings everyone. Welcome to this tutorial on Edit molecules.
00:08 In this tutorial, we will learn to- add and delete atoms,
00:14 add and delete bonds,
00:16 rotate bonds,
00:18 change length of the bond,
00:20 change hydrogen to methyl group,
00:23 copy, paste and join structures.
00:27 Here I am using:

Ubuntu Linux OS version. 14.04,

Avogadro version 1.1.1.

00:37 To follow this tutorial, you should be familiar with: Avogadro interface.
00:43 If not, for relevant tutorials, please visit our website.
00:49 Here I will show how to open Avogadro using the Terminal.
00:55 To open the terminal, press CTRL, ALT and T keys simultaneously.
01:03 Type avogadro at the prompt and press Enter.
01:08 Avogadro application window opens.
01:12 For demonstration, I will display a molecule of n-butane from the Fragment library.
01:19 Click on Build menu. Navigate to Insert->Fragment
01:25 Insert fragment dialog box appears.
01:29 From the list of fragments, double click on alkanes folder to open.
01:35 Select butane.cml from the drop down that appears.
01:41 Click on Insert button. Click on X to close Insert Fragment dialog box.
01:49 Butane molecule, highlighted in blue color, appears on the Panel.
01:54 To remove the highlighting, Press Ctrl, Shift and A keys simultaneously.
02:02 Rotate the structure using Navigation tool to get proper alignment.
02:09 We will now learn how to add atoms to the molecule.
02:14 Click on Draw tool icon on the tool bar.
02:18 Click on end Carbon atom and drag on the Panel.
02:23 A carbon atom with required hydrogens get added.
02:27 We now have a molecule of pentane on Panel.
02:32 Similarly, you can add atoms using Draw tool to make a series of alkanes.
02:39 Open a new window. Draw propane using Draw tool.
02:45 Let us delete the end Carbon atom with hydrogens to get a molecule of Ethane.
02:52 To delete atoms, click on the Selection tool icon on the tool bar.
02:57 Click and drag over the end Carbon atom to make the selection.
03:02 Selected atoms appear blue in color.
03:06 Press Backspace to delete. Alternatively, you can use clear option in Edit menu.
03:14 To redo, press Ctrl and Z keys simultaneously.
03:20 We will demonstrate on how to add and delete bonds in a molecule.
03:26 To add bonds, select the Draw tool icon on the tool bar.
03:31 Draw Settings menu opens on the left.
03:35 By default, Carbon is selected in the Element drop down list.
03:40 To introduce a double bond, select Double from Bond Order drop down.
03:46 Click on the bond between C-1 and C-2 to convert it to a double bond.
03:52 To convert double bond into a triple bond, select Triple from Bond Order.

Click on the bond.

03:59 To delete bonds, hold the right mouse button and click on the bonds.
04:04 This results in two different molecules.
04:08 Let's rejoin the molecules.
04:11 Click on Carbon of one molecule, drag and click on carbon of other molecule.
04:18 We can rotate bonds and change bond lengths using Bond Centric Manipulation tool.
04:24 Click on Bond Centric Manipulation tool on the tool bar.
04:29 Bond Centric Manipulate settings menu opens on the left.
04:34 By default, Show Angles and Snap-to Bonds are checked.
04:39 Snap-to Threshold set to 100(10 degree).
04:43 Users can make their own choice of settings as per the requirements.
04:49 To show angles, click on the bond between two atoms.
04:55 We need to fix the plane of rotation of the bonds.
04:59 To fix the plane you want, click on the bond and move upwards or downwards.
05:05 The plane between the atoms appears in blue or yellow color.
05:11 To Rotate, click on one of the atoms and move.
05:16 Attached bond along with the atoms rotates in the fixed plane.
05:21 To change length of the bond, hold the right mouse button and drag.
05:27 Now we will show how to change Hydrogens to methyl groups.
05:32 Click on Build menu and click on Change H To Methyl.
05:38 All Hydrogens are now replaced by Methyl groups.
05:43 Press CTRL and Z keys simultaneously to undo the changes.
05:49 We can also select a particular hydrogen atom and change it to a methyl group.
05:55 Click on Selection tool icon on the tool bar
05:59 Click on the hydrogen attached to end carbon atom to select.
06:04 Go to Build menu and click on Change H to Methyl.
06:10 The selected Hydrogen gets replaced by methyl group.
06:15 To deselect, Press Ctrl, Shift and A keys simultaneously.
06:22 Let us take a look as how to copy, paste and join structures.
06:28 Click on File-> New to open a new window.
06:33 We will learn to build a Maltose molecule.
06:37 Maltose is made up of two glucose molecules.
06:41 To insert a glucose molecule, click on Build menu.
06:46 Scroll down and click on Insert -> Fragment
06:51 Insert Fragment dialog box appears.
06:55 Scroll down the list and click on Cyclic sugar folders.
07:01 A sub menu appears.
07:04 Navigate down and select beta-d-glucopyranose.cml.
07:10 Click on Insert button. Close the dialog box.
07:16 beta-D-glucopyranose.cml appears on panel highlighted in blue color.
07:24 Translate it to the center, using hand tool.
07:28 Let us copy and paste another glucose molecule.
07:33 Click on Edit menu on the menu bar.
07:36 And click on Copy. Again scroll down the Edit menu and then click Paste.
07:44 Please note: during copy, paste operation, window dims for a moment and then recovers.
07:51 A new molecule gets copied and pasted on the existing molecule on the panel.
07:58 The cursor changes to a hand tool.
08:01 Move the copied molecule from the original molecule.
08:06 Now we have two separate molecules on the panel.
08:10 To de-select, press Ctrl, Shift and A keys simultaneously.
08:17 Let us label the molecules. Labeling helps to identify the positions of all the atoms.
08:25 To label, click on Label check-box from the Display Types drop down.
08:32 To get maltose, we need to remove a water molecule.
08:37 Delete the OH group on C-1 of first molecule and hydrogen on C-9 of second molecule.
08:46 Select Carbon in Draw tool settings.
08:50 Select Single as Bond Order.
08:54 Uncheck Adjust Hydrogens check box.
08:58 Click and drag to join C-1 of first molecule and C-9 of second molecule through oxygen atom.
09:07 We need to optimize the geometry.
09:11 Select Auto Optimization tool.
09:15 Auto Optimization settings menu appears on the left.
09:20 Select MMFF94 force field and click on Start.
09:27 The optimization may take a few seconds to complete. You may remove the labels now.
09:35 We now have an optimized structure of maltose on panel.
09:40 Let's summarize. In this tutorial, we have learnt to: add and delete atoms,
09:47 add and delete bonds,
09:50 rotate bonds,
09:52 change bond length,
09:54 change hydrogen to methyl group,
09:56 copy, paste and join structures.
10:00 As an assignment, create a Butane molecule using draw tool.
10:06 Convert it into 2,3 dimethyl Butane.
10:10 Rotate the bonds and change bond lengths.
10:14 Create a molecule of cellulose (Hint: D- glucose monomer is available in the Insert fragment library)
10:22 Optimize the geometry using UFF force field.
10:27 This video summarises the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
10:36 We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
10:44 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:52 This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi.

Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Avogadro/C2/Edit-molecules/English-timed&oldid=43676"