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

From Script | Spoken-Tutorial
Jump to: navigation, search
 
(One intermediate revision by the same user not shown)
Line 12: Line 12:
 
|-
 
|-
 
| 00:11
 
| 00:11
−
|Rotate, zoom in and zoom out,  
+
|'''Rotate''', '''zoom in''' and '''zoom out''',  
 
|-
 
|-
 
| 00:15
 
| 00:15
−
|Build molecules on the Panel,  
+
|build molecules on the '''panel''',  
 
|-
 
|-
 
| 00:17
 
| 00:17
−
|Set up force field and optimize geometry,  
+
|set up force field and optimize geometry,  
 
|-
 
|-
 
| 00:21
 
| 00:21
−
|Measure bond lengths, bond angles, dihedral angles,  
+
|measure '''bond''' lengths, '''bond''' angles, dihedral angles,  
 
|-
 
|-
 
| 00:25
 
| 00:25
−
|Show fragment library,  
+
|show fragment library,  
 
|-
 
|-
 
| 00:27
 
| 00:27
−
|Build DNA molecules and ''' Peptides'''.  
+
|build DNA molecules and ''' Peptides'''.  
 
|-
 
|-
 
| 00:31
 
| 00:31
−
|Here I am using ''' Ubuntu Linux OS version 14.04 ''',  
+
|Here I am using: ''' Ubuntu Linux OS version 14.04 ''',  
 
'''Avogadro''' version 1.1.1,  
 
'''Avogadro''' version 1.1.1,  
−
Working Internet connection.  
+
working internet connection.  
  
 
|-
 
|-
Line 48: Line 48:
 
|-
 
|-
 
| 01:00
 
| 01:00
−
|In the search bar, type '''  avogadro ''' .  
+
|In the '''search bar''', type '''  avogadro ''' .  
 
|-
 
|-
 
| 01:02
 
| 01:02
Line 57: Line 57:
 
|-
 
|-
 
| 01:15
 
| 01:15
−
|To '''import''' a molecule, we need a working Internet connection.  
+
|To '''import''' a molecule, we need a working internet connection.  
 
|-
 
|-
 
| 01:19
 
| 01:19
Line 73: Line 73:
 
|-
 
|-
 
| 01:30
 
| 01:30
−
|For demonstration, I will type '''  xylene'''  in the search box.  
+
|For demonstration, I will type '''  xylene'''  in the '''search box'''.  
 
|-
 
|-
 
| 01:36
 
| 01:36
Line 85: Line 85:
 
|-
 
|-
 
| 01:45
 
| 01:45
−
|Click on '''  Navigation tool ''' on the tool bar.  
+
|Click on '''  Navigation tool ''' on the '''tool bar'''.  
 
|-
 
|-
 
| 01:49
 
| 01:49
Line 118: Line 118:
 
|-
 
|-
 
| 02:37
 
| 02:37
−
|'''  Element '''  drop down list shows list of elements.  
+
|'''  Element '''  drop-down list shows list of elements.  
 
|-
 
|-
 
| 02:42
 
| 02:42
Line 127: Line 127:
 
|-
 
|-
 
| 02:51
 
| 02:51
−
|Lets draw structure of '''  Aniline '''  on the ''' Panel ''' .  
+
|Let's draw '''structure''' of '''  Aniline '''  on the ''' Panel ''' .  
 
|-
 
|-
 
| 02:55
 
| 02:55
Line 163: Line 163:
 
|-  
 
|-  
 
| 03:45
 
| 03:45
−
|We have the structure of '''  Aniline'''  on the Panel.  
+
|We have the structure of '''  Aniline'''  on the '''Panel'''.  
 
|-
 
|-
 
| 03:49
 
| 03:49
Line 190: Line 190:
 
|-
 
|-
 
| 04:33
 
| 04:33
−
|Let's measure bond lengths, bond angles and '''  dihedral angles '''  of '''  Aniline ''' .  
+
|Let's measure '''bond''' lengths, bond angles and '''  dihedral angles '''  of '''  Aniline ''' .  
 
|-
 
|-
 
| 04:40
 
| 04:40
Line 208: Line 208:
 
|-
 
|-
 
| 05:07
 
| 05:07
−
|To save the file, click on ''' File'''  and ''' Save As''' .  
+
|To '''save''' the file, click on ''' File'''  and ''' Save As''' .  
 
|-
 
|-
 
| 05:13
 
| 05:13
Line 214: Line 214:
 
|-
 
|-
 
| 05:17
 
| 05:17
−
|Type the File Name as ''' Aniline.cml''' .  
+
|Type the '''File Name''' as ''' Aniline.cml''' .  
 
|-
 
|-
 
| 05:21
 
| 05:21
Line 220: Line 220:
 
|-
 
|-
 
| 05:28
 
| 05:28
−
|Click on ''' New'''  icon to open a new window.  
+
|Click on ''' New'''  icon to open a new '''window'''.  
 
|-
 
|-
 
| 05:32
 
| 05:32
Line 238: Line 238:
 
|-
 
|-
 
| 05:55
 
| 05:55
−
|For example let's open ''' alkenes ''' folder.  
+
|For example, let's open ''' alkenes ''' folder.  
 
|-
 
|-
 
| 06:00
 
| 06:00
Line 259: Line 259:
 
|-
 
|-
 
| 06:26
 
| 06:26
−
|We can build many natural products using '''  Isoprene '''  
+
|We can build many natural products using '''  Isoprene '''.
 
|-
 
|-
 
| 06:30
 
| 06:30
Line 274: Line 274:
 
|-
 
|-
 
| 06:51
 
| 06:51
−
|I will translate ''' Isoprene ''' to a corner.  
+
|I will '''translate''' ''' Isoprene ''' to a corner.  
 
|-
 
|-
 
| 06:56
 
| 06:56
Line 289: Line 289:
 
|-
 
|-
 
| 07:16
 
| 07:16
−
|Using '''  porphyrin '''  fragment, we can build complex chemical structures: Such as '''  Chlorophyll '''  and '''  Vitamin B12 ''' .  
+
|Using '''  porphyrin '''  fragment, we can build complex chemical structures such as: '''  Chlorophyll '''  and '''  Vitamin B12 ''' .  
 
|-
 
|-
 
| 07:25
 
| 07:25
Line 313: Line 313:
 
|-
 
|-
 
| 08:00
 
| 08:00
−
|Four ''' nucleic acid bases ''' are shown as buttons.  
+
|Four ''' nucleic acid bases ''' are shown as '''button'''s.  
 
|-
 
|-
 
| 08:05
 
| 08:05
−
|Click on the buttons to choose the ''' nucleic acid ''' sequence.  
+
|Click on the buttons to choose the ''' nucleic acid ''' '''sequence'''.  
 
|-
 
|-
 
| 08:10
 
| 08:10
Line 328: Line 328:
 
|-
 
|-
 
| 08:32
 
| 08:32
−
|In the '''  Bases Per Turn '''  drop down, select A, select "5": which is the number of base pairs per '''  Helix ''' .  
+
|In the '''  Bases Per Turn '''  drop down, select A, select "5" which is the number of base pairs per '''  Helix ''' .  
 
|-
 
|-
 
| 08:41
 
| 08:41
Line 343: Line 343:
 
|-
 
|-
 
| 09:01
 
| 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
 
| 09:09
Line 388: Line 388:
 
|-
 
|-
 
| 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,  
 
|-
 
|-
 
| 10:37
 
| 10:37
Line 409: Line 409:
 
|-
 
|-
 
| 10:41
 
| 10:41
−
|As an assignment - Create a protein sequence using the following amino acid residues:  
+
|As an assignment - Create a '''protein sequence''' using the following amino acid residues:  
 
|-
 
|-
 
| 10:49
 
| 10:49
Line 415: Line 415:
 
|-
 
|-
 
| 10:53
 
| 10:53
−
|Save the image as ''' .cml '''file.  
+
|'''Save''' the image as ''' .cml '''file.  
 
|-
 
|-
 
| 10:58
 
| 10:58
Line 424: Line 424:
 
|-
 
|-
 
| 11:10
 
| 11:10
−
|Save the image as ''' .cml ''' file.  
+
|'''Save''' the '''image''' as ''' .cml ''' file.  
 
|-
 
|-
 
| 11:14
 
| 11:14
−
|This video summarizes the '''Spoken Tutorial''' project.  
+
|This '''video''' summarizes the '''Spoken Tutorial''' project.  
 
|-
 
|-
 
| 11:18
 
| 11:18
−
|If you do not have good bandwidth, you can download and watch it.  
+
|If you do not have good '''bandwidth''', you can '''download''' and watch it.  
 
|-
 
|-
 
| 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

Latest revision as of 15:48, 5 July 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 Let's 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 deselect 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

Retrieved from "https://script.spoken-tutorial.org/index.php?title=Avogadro/C2/Build-molecules/English-timed&oldid=43662"