Sandhya.np14 at 16:16, 6 July 2018

2018-07-06T16:16:55Z

Sandhya.np14 at 12:39, 6 July 2018

2018-07-06T12:39:28Z

Sandhya.np14 at 09:11, 5 June 2018

2018-06-05T09:11:01Z

PoojaMoolya: 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..."

2017-07-21T11:42:43Z

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..."

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{| border=1
||'''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

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|| 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'''.

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|| 00:55
|| To open the terminal press '''CTRL, ALT''' and '''T '''keys simultaneously.

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|| 01:03
|| Type '''avogadro '''at the prompt and press enter.

|-
|| 01:08
||'''Avogadro''' application window opens.

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|| 01:12
|| For demonstration, I will display a molecule of '''n-butane''' from the '''Fragment''' library.

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|| 01:19
|| Click on '''Build''' menu. Navigate to '''Insert->Fragment'''

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|| 01:25
||'''Insert fragment''' dialog box appears.

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|| 01:29
|| From the list of fragments, double click on '''alkanes''' folder to open.

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|| 01:35
||Select '''butane.cml''' from the drop down that appears.

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|| 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.

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||02:09
|| We will now learn how to add atoms to the molecule.

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|| 02:14
|| Click on '''Draw tool''' icon on the tool bar.

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|| 02:18
|| Click on end '''Carbon''' atom and drag on the '''Panel.'''

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|| 02:23
||A carbon atom with required hydrogens get added.

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|| 02:27
|| We now have a molecule of '''pentane''' on '''Panel'''.

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|| 02:32
||Similarly, you can add atoms using '''Draw tool''' to make a series of alkanes.

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|| 02:39
|| Open a new window. Draw propane using '''Draw tool.'''

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|| 02:45
|| Let us delete the end Carbon atom with hydrogens to get a molecule of '''Ethane'''.

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|| 02:52
|| To delete atoms, click on the '''Selection tool''' icon on the tool bar.

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|| 02:57
|| Click and drag over the end Carbon atom to make the selection.

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|| 03:02
||Selected atoms appears blue in color.

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|| 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.

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|| 03:20
|| We will demonstrate on how to add and delete bonds in a molecule.

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|| 03:26
|| To add bonds select the '''Draw tool''' icon on the tool bar.

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|| 03:31
||'''Draw Settings''' menu open on the left.

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|| 03:35
|| By default '''Carbon''' is selected in the '''Element '''drop down list.

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|| 03:40
||To introduce a double bond select '''Double''' from '''Bond Order '''drop down.

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|| 03:46
|| Click on the bond between C-1 and C-2 to convert it to a double bond.

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|| 03:52
|| To convert double bond into a triple bond, select '''Triple''' from '''Bond Order.'''

Click on the bond.

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|| 03:59
|| To delete bonds, hold the right mouse button and click on the bonds.

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|| 04:04
||This results in two different molecules.

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|| 04:08
|| Let's rejoin the molecules.

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|| 04:11
|| Click on Carbon of one molecule, drag and click on carbon of other molecule.

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|| 04:18
|| We can rotate bonds and change bond lengths using '''Bond Centric Manipulation''' tool.

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|| 04:24
|| Click on '''Bond Centric Manipulation tool''' on the tool bar.

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|| 04:29
|| '''Bond Centric Manipulate '''settings menu opens on the left.

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|| 04:34
|| By default, '''Show Angles''' and '''Snap-to Bonds''' are checked.

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|| 04:39
||'''Snap-to Threshold''' set to '''10<sup>0'''</sup>(10 degree).

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|| 04:43
||Users can make their own choice of settings as per the requirements.

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|| 04:49
|| To show angles, click on the bond between two atoms.

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|| 04:55
|| We need to fix the plane of rotation of the bonds.

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||04:59
|| To fix the plane you want, click on the bond and move upwards or downwards.

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|| 05:05
||The plane between the atoms appears in blue or yellow color.

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|| 05:11
|| To Rotate, click on one of the atoms and move.

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|| 05:16
||Attached bond along with the atoms rotates in the fixed plane.

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|| 05:21
|| To change length of the bond hold the right mouse button and drag.

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|| 05:27
|| Now we will show how to change Hydrogens to methyl groups.

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|| 05:32
|| Click on '''Build ''' menu and click on '''Change H To Methyl.'''

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|| 05:38
|| All '''Hydrogens''' are now replaced by '''Methyl''' groups.

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|| 05:43
||Press '''CTRL''' and ''' Z keys''' simultaneously to undo the changes.

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||05:49
|| We can also select a particular '''hydrogen''' atom and change it to a '''methyl''' group.

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||05:55
|| Click on '''Selection tool ''' icon on the tool bar

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|| 05:59
|| Click on the '''hydrogen''' attached to end carbon atom to select.

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|| 06:04
|| Go to '''Build''' menu and click on '''Change H to Methyl'''.

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|| 06:10
||The selected '''Hydrogen''' gets replaced by '''methyl''' group.

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|| 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.

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|| 06:28
|| Click on '''File'''-> '''New''' to open a new window.

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|| 06:33
|| We will learn to build a '''Maltose''' molecule.

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|| 06:37
||'''Maltose''' is made up of two '''glucose''' molecules.

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|| 06:41
|| To insert a '''glucose''' molecule, click on '''Build''' menu.

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|| 06:46
|| Scroll down and click on '''Insert''' -> '''Fragment'''

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|| 06:51
|| '''Insert''' -> '''Fragment''' dialog box appears.

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|| 06:55
|| Scroll down the list and click on '''Cyclic sugar''' folders.

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|| 07:01
|| A sub menu appears.

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|| 07:04
|| Navigate down and select '''beta-d-glucopyranose.cml.'''

|-
|| 07:10
||Click on '''Insert''' button. Close the dialog box.

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|| 07:16
|| '''beta-D-glucopyranose.cml''' appears on panel highlighted in blue color.

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|| 07:24
||Translate it to the center using hand tool.

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|| 07:28
|| Let us copy and paste another '''glucose''' molecule.

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|| 07:33
|| Click on '''Edit''' menu on the menu bar.

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|| 07:36
|| And click on '''Copy'''.Again Scroll down the edit menu and then click '''Paste'''.

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|| 07:44
|| Please note during copy, paste operation, window dims for a moment and then recovers.

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|| 07:51
|| A new molecule gets copied and pasted on the existing molecule on the Panel.

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|| 07:58
|| The cursor changes to a hand tool.

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|| 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.
|-
|}

@@ Line 352: / Line 352: @@
 |-
 || 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
-|| 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
-|| 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
-||Now we have two separate molecules on the Panel.
+||Now we have two separate molecules on the panel.
 |-
 || 08:10
-|| To de-select Press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
+|| To de-select, press '''Ctrl, Shift ''' and '''A''' keys simultaneously.
 |-
@@ Line 384: / Line 384: @@
 |-
 || 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
-|| To get '''Maltose''', we need to remove a water molecule.
+|| 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.
+|| Delete the '''OH''' group on '''C-1''' of first molecule and hydrogen on '''C-9''' of second molecule.
 |-
@@ Line 406: / Line 406: @@
 |-
 || 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 430: / Line 430: @@
 |-
 || 09:35
-|| We now have an optimized structure of '''Maltose''' on Panel.
+|| We now have an optimized structure of '''maltose''' on panel.
 |-
@@ Line 438: / Line 438: @@
 |-
 || 09:47
-||add and delete bonds,
+||add and delete '''bond'''s,
 |-
@@ Line 450: / Line 450: @@
 |-
 || 09:54
-||change Hydrogen to Methyl group,
+||change hydrogen to methyl group,
 |-
@@ Line 458: / Line 458: @@
 |-
 || 10:00
-|| As an assignment, create a '''Butane''' molecule using draw tool.
+|| As an assignment, create a '''Butane''' molecule using '''draw''' tool.
 |-
@@ Line 470: / Line 470: @@
 |-
 || 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)
 |-

@@ Line 316: / Line 316: @@
 |-
 || 06:51
-|| '''Insert''' -> '''Fragment''' dialog box appears.
+|| '''Insert Fragment''' dialog box appears.
 |-

Avogadro/C2/Edit-molecules/English-timed - Revision history

Sandhya.np14 at 16:16, 6 July 2018

Sandhya.np14 at 12:39, 6 July 2018

Sandhya.np14 at 09:11, 5 June 2018

PoojaMoolya: 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..."