Sandhya.np14 at 10:18, 5 July 2018

2018-07-05T10:18:23Z

Sandhya.np14 at 07:58, 5 June 2018

2018-06-05T07:58:57Z

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Sandhya.np14 at 14:58, 19 April 2018

2018-04-19T14:58:50Z

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PoojaMoolya: Created page with "{| border =1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings everyone!! Welcome to this tutorial on ''' Build Molecules '''. |- | 00:07 |In this tutorial, we will..."

2017-07-21T12:08:11Z

Created page with "{| border =1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings everyone!! Welcome to this tutorial on ''' Build Molecules '''. |- | 00:07 |In this tutorial, we will..."

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

|-
| 00:01
|Warm greetings everyone!! Welcome to this tutorial on ''' Build Molecules '''.

|-
| 00:07
|In this tutorial, we will learn to: Import molecules from database
|-
| 00:11
|Rotate, zoom in and zoom out
|-
| 00:15
|Build molecules on the Panel
|-
| 00:17
|Set up force field and optimize geometry
|-
| 00:21
|Measure bond lengths, bond angles, dihedral angles
|-
| 00:25
|Show fragment library
|-
| 00:27
|Build DNA molecules and ''' Peptides ''' .
|-
| 00:31
|Here I am using ''' Ubuntu Linux OS version 14.04 '''
''' Avogadro ''' version 1.1.1
Working Internet connection.

|-
| 00:44
|To follow this tutorial you should have, knowledge of basic Chemistry.
To download ''' Avogadro ''' please use the link shown ''' sourceforge.net/projects/avogadro. '''
|-
| 00:53
|I have already downloaded ''' Avogadro '''

|-
| 00:56
|To open ''' Avogadro ''' , click on ''' ''' Dash home ''' .

|-
| 01:00
|In the search bar, type ''' avogadro ''' .
|-
| 01:02
|Click on ''' Avogadro''' icon to open the application.
|-
| 01:08
|Let's begin by importing a ''' xylene ''' molecule from ''' chemical structure database ''' .
|-
| 01:15
|To import a molecule, we need a working Internet connection.
|-
| 01:19
|Click on ''' File ''' menu, navigate to ''' Import '''
|-
| 01:23
|A sub-menu opens.
|-
| 01:25
|Select ''' Fetch by chemical name ''' .

|-
| 01:28
|''' Chemical name ''' dialog box appears.
|-
| 01:30
|For demonstration I will type ''' xylene''' in the search box.
|-
| 01:36
|Click on ''' OK ''' button.
|-
| 01:38
|We now have a ''' xylene ''' molecule on the ''' Panel ''' .
|-
| 01:42
|Let's rotate the molecule on the ''' Panel''' .

|-
| 01:45
|Click on ''' Navigation tool ''' on the tool bar.
|-
| 01:49
|Place the cursor on the molecule.
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| 01:52
|Hold the left mouse button and drag.
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| 01:56
|Notice the direction arrows indicating the drag.
|-
| 02:00
|To translate the molecule, use right mouse button and drag.
|-
| 02:06
|Scroll the mouse wheel to zoom in and zoom out the structure.
|-
| 02:10
|Let's learn how to create a molecule.
|-
| 02:14
|To create a molecule, click on ''' Draw Tool ''' icon on the tool bar.
|-
| 02:19
|Under ''' Draw Settings ''' menu, we can see
''' Element ''' drop down button
''' Bond Order ''' drop down button
''' Adjust Hydrogens ''' check box.
|-
| 02:30
|If you don't want hydrogens on the structure, un-check ''' Adjust Hydrogens ''' check box.
|-
| 02:37
|''' Element ''' drop down list shows list of elements.
|-
| 02:42
|Click on ''' Other ''' to view the entire ''' Periodic table ''' in a separate window.
|-
| 02:48
|Click on ''' Close''' (X) to close the window.
|-
| 02:51
|Lets draw structure of ''' Aniline ''' on the ''' Panel ''' .
|-
| 02:55
|Select ''' Carbon ''' from ''' Element ''' drop down list.
|-
| 02:59
|Select ''' Single ''' from ''' Bond Order ''' drop down.
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| 03:03
|Click on the ''' Panel ''' .
|-
| 03:05
|Drag and drop to make a closed chain of six carbon atoms.
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| 03:10
|To show double bonds, select ''' Double ''' from ''' Bond Order ''' drop down.
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| 03:16
|Click on alternate bonds to obtain ''' Benzene ''' structure.
|-
| 03:21
|Let's complete''' Aniline ''' structure.
|-
| 03:24
|Select ''' Nitrogen ''' from ''' Element ''' drop down list.
|-
| 03:29
|Select ''' Single ''' from ''' Bond Order ''' drop down.
|-
| 03:33
|Click on any one of the carbon atoms on the structure and drag.
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| 03:39
|Go to ''' Build ''' menu and select ''' Add Hydrogens ''' .
|-
| 03:45
|We have the structure of ''' Aniline''' on the Panel.
|-
| 03:49
|To get a stable conformation, ''' Aniline ''' structure on the ''' Panel''' needs to be optimized.
|-
| 03:56
|To optimize, click on ''' Auto Optimization Tool ''' on the tool bar.
|-
| 04:02
|''' AutoOptimization Settings ''' menu appears on the left.
|-
| 04:06
|Click on ''' Force Field ''' drop down list, select ''' MMFF94 ''' .
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| 04:13
|''' MMFF94 ''' is generally used to optimize small organic molecules.
|-
| 04:20
|Click on ''' Start''' button.
|-
| 04:23
|It will take a few seconds to complete the optimization.
|-
| 04:28
|Click on ''' Stop ''' to close the ''' Optimization Settings.'''
|-
| 04:33
|Let's measure bond lengths, bond angles and ''' dihedral angles ''' of ''' Aniline ''' .
|-
| 04:40
|Select ''' Click to Measure ''' icon on the tool bar.
|-
| 04:44
|To measure distance, click on any two consecutive carbon atoms.
|-
| 04:49
|To measure angles, click on any 3 consecutive atoms.
|-
| 04:55
|To measure ''' dihedral angles, ''' click on any 4 consecutive atoms.
|-
| 05:02
|Measured values appear at the bottom of the ''' Panel''' .
|-
| 05:07
|To save the file, click on ''' File''' and ''' Save As''' .
|-
| 05:13
|''' Save Molecule As''' dialog box appears.
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| 05:17
|Type the File Name as ''' Aniline.cml''' .
|-
| 05:21
|Choose the location as ''' Desktop''' and click on ''' Save''' button.
|-
| 05:28
|Click on ''' New''' icon to open a new window.
|-
| 05:32
|''' Avogadro ''' software has a feature to build complex molecules using ''' fragment ''' library.
|-
| 05:38
|Go to ''' Build ''' menu.
|-
| 05:40
|Navigate to ''' Insert ''' and select''' Fragment ''' option.
|-
| 05:45
|''' Insert Fragment ''' dialog box opens.
|-
| 05:49
|We can see list of folders having ''' cml ''' files of different chemical structures.
|-
| 05:55
|For example let's open ''' alkenes ''' folder.
|-
| 06:00
|Double click on the folder to view the contents of the folder.
|-
| 06:04
|Select ''' 2-methyl-buta-1,3-diene.cml ''' .
|-
| 06:10
|Click on ''' Insert ''' button.
|-
| 06:13
|Click on ''' Close ''' to close the dialog box.
|-
| 06:17
|''' 2-methyl-1,3-butadiene ''' structure is displayed on the ''' Panel ''' .

|-
| 06:22
|It is commonly called as ''' Isoprene.'''
|-
| 06:26
|We can build many natural products using ''' Isoprene '''
|-
| 06:30
|The molecule is in select mode.
|-
| 06:33
|To de-select, press''' CTRL, SHIFT ''' and ''' A ''' keys simultaneously.
|-
| 06:39
|As an example: I will show ''' Vitamin A and natural rubber ''' which were built using ''' Isoprene ''' .
|-
| 06:47
|''' Vitamin A, natural rubber ''' .
|-
| 06:51
|I will translate ''' Isoprene ''' to a corner.
|-
| 06:56
|Click on ''' Build ''' menu, navigate to ''' Insert ''' and select ''' Fragment ''' .
|-
| 07:02
|Scroll down to ''' macrocycles ''' folder; double click to open.
|-
| 07:08
|Select ''' porphin ''' fragment and click on ''' Insert''' .
|-
| 07:14
|Close the dialog box.
|-
| 07:16
|Using ''' porphyrin ''' fragment, we can build complex chemical structures: Such as ''' Chlorophyll ''' and ''' Vitamin B12 ''' .
|-
| 07:25
|''' Chlorophyll '''
|-
| 07:27
|''' Vitamin B12.'''
|-
| 07:30
|Complex molecules like ''' DNA ''' and ''' peptides ''' can be easily built using ''' Avogadro ''' .
|-
| 07:37
|Open a new window using ''' New ''' icon.
|-
| 07:41
|To insert a ''' DNA ''' molecule, go to ''' Build ''' menu navigate to ''' Insert ''' and click on ''' ''' DNA/RNA ''' from the sub-menu.
|-
| 07:51
|''' Insert Nucleic Acids ''' dialog box appears.
|-
| 07:55
|Select ''' DNA ''' from ''' DNA/RNA Builder''' drop down.
|-
| 08:00
|Four ''' nucleic acid bases ''' are shown as buttons.
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| 08:05
|Click on the buttons to choose the ''' nucleic acid ''' sequence.
|-
| 08:10
|You can choose your own sequence of ''' acids''' .
|-
| 08:14
|For demonstration I will select ''' A T G C A T G C.'''
|-
| 08:26
|The order of selection of ''' nucleic acids ''' appear in the ''' Sequence ''' text box.
|-
| 08:32
|In the ''' Bases Per Turn ''' drop down, select A, select "5": which is the number of base pairs per ''' Helix ''' .
|-
| 08:41
|Select ''' Strands ''' as ''' Single ''' and click on ''' Insert ''' button.
|-
| 08:47
|Click on ''' Close''' to close the dialog box.
|-
| 08:51
|We now have a single stranded ''' DNA ''' molecule on the ''' Panel ''' .
|-
| 08:56
|Zoom out the structure and drag to the center of the ''' Panel ''' .
|-
| 09:01
|To deselected the ''' DNA ''' molecule on the ''' Panel ''' , press ''' CTRL, Shift ''' and ''' A ''' keys simultaneously.
|-
| 09:09
|We can also create a ''' Peptide ''' sequence using ''' Peptide ''' option in the ''' Insert ''' menu.
|-
| 09:16
|Again click on ''' New ''' icon to open a new window.
|-
| 09:21
|Go to ''' Build ''' menu scroll down to ''' Insert ''' and ''' Peptide ''' .
|-
| 09:26
|''' Insert Peptide ''' dialog box appears.
|-
| 09:29
|Select ''' amino acids ''' for the ''' Peptide''' sequence by clicking on the ''' amino acids ''' buttons.
|-
| 09:36
|For demonstration I will choose the sequence as ''' Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys) ''' .
|-
| 09:45
|The order of selection appear in the ''' Sequence ''' text box.
|-
| 09:50
|Click on ''' Insert Peptide ''' button.
|-
| 09:53
|Close the ''' Insert Peptide ''' dialog box.
|-
| 09:57
|''' Peptide ''' chain appears on the ''' Panel ''' .
|-
| 10:00
|To de-select the ''' Peptide ''' on ''' Panel ''' , press ''' CTRL, Shift ''' and ''' A ''' keys simultaneously.
|-
| 10:07
|You can choose the''' amino acids ''' of your choice and build the ''' Peptide ''' sequence.
|-
| 10:13
|Let's summarize.
|-
| 10:15
|In this tutorial we learnt to :
|-
| 10:18
|Import molecules from the database
|-
| 10:21
|Rotate, zoom in and zoom out
|-
| 10:24
|Build molecules on the panel
|-
| 10:26
|Set up force field and optimize geometry
|-
| 10:30
|Measure bond lengths, bond angles, dihedral angles
|-
| 10:35
|Show fragment library
|-
| 10:37
|Build ''' DNA ''' molecules and ''' Peptides ''' .
|-
| 10:41
|As an assignment - Create a protein sequence using the following amino acid residues:
|-
| 10:49
|Optimize the geometry using ''' UFF''' force field
|-
| 10:53
|Save the image as ''' .cml ''' file.
|-
| 10:58
| Build ''' RNA ''' sequence using the ''' Nucleic acids: AUGC '''

|-
| 11:04
|Optimize geometry using ''' MMFF94 ''' force field

|-
| 11:10
|Save the image as ''' .cml ''' file.

|-
| 11:14
|This video summarizes the Spoken Tutorial project
|-
| 11:18
|If you do not have good bandwidth, you can download and watch it.
|-
| 11:23
|We conduct workshops using Spoken Tutorials and give certificates. Please contact us.

|-
| 11:30
|Spoken Tutorial Project is funded by ''' NMEICT, MHRD Government of ''' India
|-
| 11:36
|This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.
|}

@@ Line 343: / Line 343: @@
 |-
 | 09:01
-|To deselected the ''' DNA ''' molecule on the '''  Panel ''' , press ''' CTRL, Shift ''' and ''' A ''' keys simultaneously.
+|To deselect the ''' DNA ''' molecule on the '''  Panel ''' , press ''' CTRL, Shift ''' and ''' A ''' keys simultaneously.
 |-
 | 09:09

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

Sandhya.np14 at 10:18, 5 July 2018

Sandhya.np14 at 07:58, 5 June 2018

Sandhya.np14 at 14:58, 19 April 2018

PoojaMoolya: Created page with "{| border =1 |'''Time''' |'''Narration''' |- | 00:01 |Warm greetings everyone!! Welcome to this tutorial on ''' Build Molecules '''. |- | 00:07 |In this tutorial, we will..."