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

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(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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|Warm greetings everyone!!  Welcome to this tutorial on ''' Build Molecules '''.  
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|Warm greetings everyone!!  Welcome to this tutorial on ''' Build Molecules'''.  
  
 
|-
 
|-
 
| 00:07
 
| 00:07
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|In this tutorial, we will learn to: Import molecules from database  
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|In this tutorial, we will learn to: '''Import''' molecules from database,
 
|-
 
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| 00:11
 
| 00:11
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|Rotate, zoom in and zoom out  
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|Rotate, zoom in and zoom out,
 
|-
 
|-
 
| 00:15
 
| 00:15
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|Build molecules on the Panel  
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|Build molecules on the Panel,
 
|-
 
|-
 
| 00:17
 
| 00:17
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|Set up force field and optimize geometry  
+
|Set up force field and optimize geometry,
 
|-
 
|-
 
| 00:21
 
| 00:21
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|Measure bond lengths, bond angles, dihedral angles  
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|Measure bond lengths, bond angles, dihedral angles,
 
|-
 
|-
 
| 00:25
 
| 00:25
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|Show fragment library  
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|Show fragment library,
 
|-
 
|-
 
| 00:27
 
| 00:27
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|Build DNA molecules and ''' Peptides ''' .  
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|Build DNA molecules and ''' Peptides'''.  
 
|-
 
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| 00:31
 
| 00:31
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|Here I am using ''' Ubuntu Linux OS version 14.04 '''  
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|Here I am using ''' Ubuntu Linux OS version 14.04 ''',
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''' Avogadro ''' version 1.1.1  
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'''Avogadro''' version 1.1.1,
 
Working Internet connection.  
 
Working Internet connection.  
  
 
|-
 
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| 00:44
 
| 00:44
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|To follow this tutorial you should have, knowledge of basic Chemistry.  
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|To follow this tutorial, you should have knowledge of basic Chemistry.  
−
To download '''  Avogadro ''' please use the link shown ''' sourceforge.net/projects/avogadro. '''  
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To download '''  Avogadro,''' please use the link shown '''sourceforge.net/projects/avogadro.'''  
 
|-
 
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| 00:53
 
| 00:53
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|I have already downloaded ''' Avogadro '''  
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|I have already downloaded ''' Avogadro.'''  
  
 
|-
 
|-
 
| 00:56
 
| 00:56
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|To open ''' Avogadro ''' , click on '''  '''  Dash home ''' .  
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|To open '''Avogadro ''' , click on '''  Dash home ''' .  
  
 
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| 01:02
 
| 01:02
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|Click on '''  Avogadro'''  icon to open the application.  
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|Click on '''  Avogadro'''  icon to open the '''application'''.  
 
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| 01:08
 
| 01:08
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|-
 
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| 01:15
 
| 01:15
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|To import a molecule, we need a working Internet connection.  
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|To '''import''' a molecule, we need a working Internet connection.  
 
|-
 
|-
 
| 01:19
 
| 01:19
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|Click on ''' File '''  menu, navigate to '''  Import '''  
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|Click on '''File'''  menu, navigate to '''  Import '''.
 
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| 01:23
 
| 01:23
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| 01:30
 
| 01:30
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|For demonstration I will type '''  xylene'''  in the search box.  
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|For demonstration, I will type '''  xylene'''  in the search box.  
 
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| 01:36
 
| 01:36
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| 01:42
 
| 01:42
 
|Let's rotate the molecule on the ''' Panel''' .  
 
|Let's rotate the molecule on the ''' Panel''' .  
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| 01:45
 
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| 01:52
 
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|Hold the left mouse button and drag.  
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|Hold the left '''mouse''' button and drag.  
 
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| 01:56
 
| 01:56
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| 02:00
 
| 02:00
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|To translate the molecule, use right mouse button and drag.  
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|To '''translate''' the molecule, use right '''mouse''' button and drag.  
 
|-
 
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| 02:06
 
| 02:06
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|Scroll the mouse wheel to zoom in and zoom out the structure.  
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|Scroll the mouse wheel to '''zoom in''' and '''zoom out''' the structure.  
 
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| 02:10
 
| 02:10
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| 02:19
 
| 02:19
 
|Under '''  Draw Settings ''' menu, we can see  
 
|Under '''  Draw Settings ''' menu, we can see  
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'''  Element ''' drop down button  
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'''  Element ''' drop down button,
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''' Bond Order '''  drop down button  
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''' Bond Order '''  drop down button,
 
''' Adjust Hydrogens '''  check box.  
 
''' Adjust Hydrogens '''  check box.  
 
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| 03:10
 
| 03:10
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|To show double bonds, select '''  Double '''  from '''  Bond Order '''  drop down.  
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|To show double-bonds, select '''  Double '''  from '''  Bond Order '''  drop-down.  
 
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|Click on '''  Force Field '''  drop down list, select '''  MMFF94 ''' .  
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|Click on '''  Force Field '''  drop-down list, select '''  MMFF94 ''' .  
 
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|''' Save Molecule As'''  dialog box appears.  
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|''' Save Molecule As'''  dialog-box appears.  
 
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|''' 2-methyl-1,3-butadiene ''' structure is displayed on the ''' Panel ''' .  
 
|''' 2-methyl-1,3-butadiene ''' structure is displayed on the ''' Panel ''' .  
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| 06:39
 
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|As an example: I will show ''' Vitamin A and natural rubber ''' which were built using ''' Isoprene ''' .  
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|As an example: I will show '''Vitamin A and natural rubber''' which were built using '''Isoprene''' .  
 
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| 07:41
 
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|To insert a '''  DNA '''  molecule, go to '''  Build '''  menu navigate to ''' Insert ''' and click on '''  ''' DNA/RNA ''' from the sub-menu.  
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|To insert a '''  DNA '''  molecule, go to '''  Build '''  menu, navigate to ''' Insert ''' and click on '''  ''' DNA/RNA ''' from the sub-menu.  
 
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|For demonstration I will select '''  A T G C A T G C.'''   
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|For demonstration, I will select '''  A T G C A T G C.'''   
 
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| 08:56
 
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|Zoom out the structure and drag to the center of the '''  Panel ''' .  
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|'''Zoom out''' the structure and drag to the center of the '''  Panel ''' .  
 
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|Go to ''' Build ''' menu scroll down to ''' Insert ''' and ''' Peptide ''' .  
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|Go to ''' Build ''' menu, scroll down to ''' Insert ''' and ''' Peptide ''' .  
 
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|Select ''' amino acids ''' for the ''' Peptide'''  sequence by clicking on the ''' amino acids ''' buttons.  
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|Select ''' amino acids ''' for the ''' Peptide'''  sequence by clicking on the ''' amino acids ''' button.  
 
|-
 
|-
 
| 09:36
 
| 09:36
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|For demonstration I will choose the sequence as '''  Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys) ''' .  
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|For demonstration, I will choose the sequence as '''  Glycine(Gly) -Valine(Val) -Proline(Pro) and Cystine(Cys) ''' .  
 
|-
 
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| 09:45
 
| 09:45
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|The order of selection appear in the '''  Sequence ''' text box.  
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|The order of selection appears in the '''  Sequence ''' text box.  
 
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| 09:50
 
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| 10:15
 
| 10:15
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|In this tutorial we learnt to :  
+
|In this tutorial, we learnt to :  
 
|-
 
|-
 
| 10:18
 
| 10:18
−
|Import molecules from the database  
+
|Import molecules from the database,
 
|-
 
|-
 
| 10:21
 
| 10:21
−
|Rotate, zoom in and zoom out  
+
|Rotate, zoom in and zoom out,
 
|-
 
|-
 
| 10:24
 
| 10:24
−
|Build molecules on the panel  
+
|Build molecules on the panel,
 
|-
 
|-
 
| 10:26
 
| 10:26
−
|Set up force field and optimize geometry  
+
|Set up force field and optimize geometry,
 
|-
 
|-
 
| 10:30
 
| 10:30
−
|Measure bond lengths, bond angles, dihedral angles  
+
|Measure bond lengths, bond angles, dihedral angles,
 
|-
 
|-
 
| 10:35
 
| 10:35
−
|Show fragment library  
+
|Show fragment library,
 
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| 10:37
 
| 10:37
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| 10:49
 
| 10:49
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|Optimize the geometry using ''' UFF''' force field  
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|Optimize the geometry using ''' UFF''' force field.
 
|-
 
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| 10:53
 
| 10:53
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|Save the image as ''' .cml ''' file.  
+
|Save the image as ''' .cml '''file.  
 
|-
 
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| 10:58
 
| 10:58
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| Build '''  RNA '''  sequence using the '''  Nucleic acids: AUGC '''  
+
| Build '''  RNA '''  sequence using the '''  Nucleic acids: AUGC '''.
−
 
+
 
|-
 
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| 11:04
 
| 11:04
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|Optimize geometry using ''' MMFF94 ''' force field  
+
|Optimize geometry using '''MMFF94 '''force field.
−
 
+
 
|-
 
|-
 
| 11:10
 
| 11:10
 
|Save the image as ''' .cml ''' file.  
 
|Save the image as ''' .cml ''' file.  
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|-
 
|-
 
| 11:14
 
| 11:14
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|This video summarizes the Spoken Tutorial project  
+
|This video summarizes the '''Spoken Tutorial''' project.
 
|-
 
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| 11:18
 
| 11:18
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| 11:23
 
| 11:23
 
|We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
 
|We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
−
 
 
|-
 
|-
 
| 11:30
 
| 11:30
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|Spoken Tutorial Project is funded by '''  NMEICT, MHRD Government of '''  India  
+
|Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
 
|-
 
|-
 
| 11:36
 
| 11:36
 
|This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.  
 
|This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.  
 
|}
 
|}

Revision as of 20:28, 19 April 2018

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.
01:52 Hold the left mouse button and drag.
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.
03:03 Click on the Panel .
03:05 Drag and drop to make a closed chain of six carbon atoms.
03:10 To show double-bonds, select Double from Bond Order drop-down.
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.
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 .
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.
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.
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 button.
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 appears 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.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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