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

Nancyvarkey at 02:15, 1 January 2016

2016-01-01T02:15:06Z

Madhurig: Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' || Warm greetings everyone!! Welcome to this tutorial on '''Build Molecules'''...."

2015-12-31T06:00:21Z

Created page with "{| border=1 ||'''Visual Cue''' ||'''Narration''' |- ||'''Slide Number 1''' '''Title Slide''' || Warm greetings everyone!! Welcome to this tutorial on '''Build Molecules'''...."

New page

{| border=1
||'''Visual Cue'''
||'''Narration'''
|-
||'''Slide Number 1'''

'''Title Slide'''
|| Warm greetings everyone!!

Welcome to this tutorial on '''Build Molecules'''.
|-
|| '''Slide Number 2'''

'''Learning Objectives'''
|| In this tutorial, we will learn to:

* Import molecules from database

* Rotate, zoom in and zoom out

* Build molecules on the Panel

* Set up force field and optimize geometry

* Measure bond lengths, bond angles, dihedral angles

* Show fragment library

* Build DNA molecules and peptides.
|-
|| '''Slide Number 3'''

'''System Requirement'''
|| Here I am using

* Ubuntu Linux OS version 14.04

* Avogadro version 1.1.1

* Working Internet connection.
|-
|| '''Slide Number 4'''

'''Pre-requisites'''
|| To follow this tutorial you should have,

* Knowledge of basic school Chemistry.
|-
|| '''Slide number 5'''

'''Download Link'''

To download '''Avogadro''' use the link shown

'''sourceforge.net/projects/avogadro'''.
|| To download '''Avogadro''' please use the link shown

'''sourceforge.net/projects/avogadro'''.

I have already downloaded Avogadro.
|-
|| Click on''' Dash home.'''
|| To open '''Avogadro, '''click on '''Dash home'''.

In the search bar, type '''avogadro'''.
|-
|| Cursor on the '''Avogadro''' icon.
|| Click on '''Avogadro''' icon to open the application window.
|-
||
|| Let's begin by importing a '''xylene''' molecule from '''chemical structure database'''.
|-
|| Cursor on the '''Panel'''.
|| To import a molecule, we need a working Internet connection.
|-
|| Click on '''File''' menu, navigate to '''Import'''.

Point to the sub-menu.
|| Click on '''File''' menu, navigate to '''Import'''.

A sub-menu opens.
|-
|| Select '''Fetch by chemical name'''.
|| Select '''Fetch by chemical name'''.
|-
|| Point to '''Chemical name''' dialog box.

Type '''xylene''' in the search box, click '''OK''' button.
|| '''Chemical name''' dialog box appears.

For demonstration I will type '''xylene''' in the search box.

Click on '''OK''' button.
|-
|| Point to '''xylene'''.
|| We now have a '''xylene''' molecule on the '''Panel'''.
|-
||
|| Let's rotate the molecule on the '''Panel'''.
|-
|| Click on '''Navigation tool''' on the tool bar.

Hold the left mouse button and drag.
|| Click on '''Navigation tool''' on the tool bar.

Place the cursor on the molecule.

Hold the left mouse button and drag.

Notice the direction arrows indicating the drag.
|-
|| Show the translation.
|| To translate the molecule, use right mouse button and drag.
|-
|| Scroll the mouse wheel to zoom in and zoom out.
|| Scroll the mouse wheel to zoom in and zoom out the structure.
|-
|| Cursor on the '''Panel'''.
|| Let's learn how to create a molecule.
|-
|| Click on '''Draw Tool''' icon on the tool bar.
|| To create a molecule, click on '''Draw Tool''' icon on the tool bar.
|-
||Point to '''Draw Settings''' menu.

Point to drop downs.
|| Under '''Draw Settings''' menu, we can see

* '''Element''' drop down button

* '''Bond Order''' drop down button

* '''Adjust Hydrogens''' check box.
|-
|| uncheck adjust hydrogens check box
|| If you don't want hydrogens on the structure, un-check '''Adjust Hydrogens''' check box.
|-
|| Scroll down the list.

Click on '''Other''' see the '''Periodic table'''.

Click on close(X).
|| '''Element''' drop down list shows list of elements.

Click on '''Other''' to view the entire '''Periodic table''' in a separate window.

Click on close(X) to close the window.
|-
|| Cursor on the Panel.
|| Lets draw structure of '''Aniline''' on the '''Panel'''.
|-
|| Click on '''Carbon'''.

Click on the '''Panel''' and drag.
|| Select '''Carbon''' from '''Element'''drop down list.

Select '''Single''' from '''Bond Order''' drop down.

Click on the '''Panel'''.

Drag and drop to make a closed chain of six carbon atoms.
|-
|| Select '''Double''' from '''Bond Order'''.

Click on alternate positions.
||To show double bonds, select '''Double''' from '''Bond Order''' drop down.

Click on alternate bonds to obtain '''Benzene''' structure.
|-
||
|| Let's complete '''Aniline''' structure.
|-
|| Select '''Nitrogen''' from '''Element''' drop down.
|| Select '''Nitrogen''' from '''Element''' drop down list.

Select '''Single''' from '''Bond Order''' drop down.
|-
|| Click on hydrogen atoms on the structure.
|| Click on any one of the carbon atoms on the structure and drag.
|-
|| Go to '''Build''' menu, select '''Add Hydrogens'''.

Point to '''Aniline''' structure.
|| Go to '''Build''' menu and select '''Add Hydrogens'''.

We have the structure of '''Aniline''' on the Panel.
|-
|| Point to '''Aniline''' structure.
|| To get a stable conformation, '''Aniline''' structure on the '''Panel''' needs to be optimized.
|-
|| Click on '''Auto Optimization Tool''' icon on the tool bar.
|| To optimize, click on '''Auto Optimization Tool''' on the tool bar.
|-
|| Point to the menu.
|| '''AutoOptimization Settings''' menu appears on the left.
|-
|| Click on '''Force Field''' drop down list, select '''MMFF94'''.
|| Click on '''Force Field''' drop down list, select '''MMFF94'''.

'''MMFF94''' is generally used to optimize small organic molecules.
|-
|| Click on '''Start''' button.

Click on '''Stop''' to close ''' AutoOptimization Settings'''.
|| Click on '''Start''' button.

It will take a few seconds to complete the optimization.

Click on '''Stop''' to close the ''' AutoOptimization Settings'''.
|-
|| Cursor on the Panel
|| Let's measure bond lengths, bond angles and '''dihedral angles''' of '''Aniline'''.
|-
|| Select '''Click to Measure''' icon on the tool bar.

Click on any two consecutive carbon atoms.

Click on 3 consecutive atoms.

Click on 4 successive atoms.

Point to the values.
|| Select '''Click to Measure''' icon on the tool bar.

To measure distance click on any two consecutive carbon atoms.

To measure angles, click on any 3 consecutive atoms.

To measure '''dihedral angles''', click on any 4 consecutive atoms.

Measured values appear at the bottom of the '''Panel'''.
|-
|| Click on File and Save as.
|| To save the file, click on '''File''' and '''Save As'''.
|-
|| Point to the dialogue box.
|| '''Save Molecule As''' dialog box appears.
|-
|| Type the File Name as '''Aniline.cml'''.

Choose file location as '''Desktop,''' click on '''Save''' button.
|| Type the File Name as '''Aniline.cml'''.

Choose the location as '''Desktop''' and click on '''Save''' button.
|-
|| Cursor on the window.
|| Click on '''New''' icon to open a new window.
|-
|| Cursor on the '''Panel'''.
|| '''Avogadro''' software has a feature to build complex molecules using '''fragment''' library.
|-
|| Go to '''Build''' menu.

Navigate to '''Insert''' and select '''Fragment''' option.

Point to the dialog box.
|| Go to '''Build '''menu.

Navigate to '''Insert''' and select '''Fragment''' option.

'''Insert Fragment''' dialog box opens.
|-
|| Point to the list of folders.
|| we can see list of folders having '''cml''' files of different chemical structures.
|-
|| Double click on the folder to see '''.cml''' files.
|| For example let's open '''alkenes''' folder.

Double click on the folder to view the contents of the folder.
|-
|| Select '''2-methylbut-2-ene.cml'''.

Click on '''Insert '''button.

Click on close to close the dialog box.
|| Select '''2-methyl-buta-1,3-diene.cml'''.

Click on '''Insert''' button.

Click on close to close the dialog box.
|-
|| Point to the structure.
|| '''2-methyl-1,3-butadiene''' structure is displayed on the '''Panel'''.

It is commonly called as '''Isoprene'''.

We can build many natural products using '''Isoprene'''.
|-
|| Press '''CTRL+SHIFT+A'''.
|| The molecule is in select mode, to de-select

Press '''CTRL''', '''SHIFT''' and '''A''' keys simultaneously.
|-
|| Show the images of '''Vitamin A''' and '''natural rubber.'''

Point to the structure.
|| As an example:

I will show '''Vitamin A''' and '''natural rubber''' which were built using '''Isoprene'''.

'''Vitamin A''', '''natural rubber.'''

I will translate '''Isoprene''' to a corner.
|-
|| Click on '''Build''' menu, select '''Fragment.'''

Scroll down to '''macrocycles''',
|| Click on '''Build''' menu, navigate to '''Insert''' and select '''Fragment.'''

Scroll down to '''macrocycles''' folder, double click to open.
|-
|| Select '''porphin''' fragment.

|| Select '''porphin''' fragment and click on '''Insert'''.

Close the dialog box.
|-
|| Show structure of '''chlorophyl''' molecule and '''Vitamin B12''' molecules.
|| Using '''porphyrin''' fragment we can build complex chemical structures:

Such as '''Chlorophyll''' and '''Vitamin B12'''.

'''Chlorophyll'''

'''Vitamin B12'''.
|-
|| Cursor on the Panel.
|| Complex molecules like '''DNA''' and '''peptides''' can be easily built using '''Avogadro'''.

Open a new window using '''New''' icon.
|-
|| Cursor on the menu bar.

Go to '''Build '''menu, '''Insert'''.

Select '''DNA/RNA''' from sub-menu.
|| To insert a '''DNA''' molecule, go to '''Build''' menu navigate to '''Insert'''

Select '''DNA/RNA''' from the sub-menu.
|-
|| Point to the box.
|| '''Insert Nucleic Acids''' dialog box appears.
|-
|| Select '''DNA in DNA/RNA builder'''.
|| Select '''DNA''' from '''DNA/RNA Builder''' drop down.
|-
|| Click on buttons.
|| Four '''nucleic acid bases''' are shown as buttons.

Click on the buttons to choose the '''nucleic acid''' sequence.
|-
|| Point to the molecule.
|| You can choose your own sequence of '''nucleic acids'''.

For demonstration I will select '''ATGC ATGC'''.

The order of selection of '''nucleic acids''' appear in the '''Sequence''' text box.
|-
|| Point to '''Bases Per Turn''' drop down, '''A''', select "5":

Select '''Strands''' as '''Single''', click on '''Insert''' button.
|| In the '''Bases Per Turn''' drop down, select '''A''', select "5": which is the number of base pairs per '''Helix'''.

Select '''Strands''' as '''Single''' and click on '''Insert''' button.
|-
|| Click on close(X) to close the dialog box.
|| Click on close(X) to close the dialog box.
|-
|| Point to the molecule.
|| We now have a single stranded '''DNA''' molecule on '''Panel'''.

Zoom out the structure and drag to the centre of the '''Panel'''.
|-
|| press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
|| To deselect the''' DNA''' molecule on Panel,

press '''CTRL, Shift''' and '''A''' keys simultaneously.
|-
||Click on '''New''' icon to open a new window.
|| We can also create a '''Peptide''' sequence using '''Peptide''' option in the '''Insert''' menu.

Again click on '''New''' icon to open a new window.
|-
|| Go to '''Build''' menu scroll down to, '''Insert''', '''Peptide'''.
|| Go to '''Build''' menu scroll down to '''Insert''' and '''Peptide'''.
|-
|| Point to the box.
|| '''Insert Peptide''' dialog box appears.
|-
|| Select '''amino acid''' sequence as Gly-Val-Pro-Cys, click on '''Insert Peptide''' button.
|| Select '''amino acids''' for the '''peptide''' sequence by clicking on the '''amino acids''' buttons.

For demonstration I will choose the sequence as '''Glycine(Gly)''' -'''Valine(Val)''' -'''Proline(Pro)''' and '''Cystine(Cys)'''.
|-
|| Point to the '''Sequence''' text box.

Click on''' Insert Peptide''' button.
|| The order of selection appear in the '''Sequence''' text box.

Click on''' Insert Peptide''' button.

Close the '''Insert Peptide''' dialog box.
|-
|| Point to the '''Peptide '''chain.

To de-select the '''Peptide''' on '''Panel''',

press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
|| '''Peptide''' chain appears on the '''Panel'''.

To de-select the '''Peptide''' on '''Panel''',

press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.

You can choose the '''amino acids''' of your choice and build the '''Peptide''' sequence.
|-
||
|| Let's summarize.
|-
|| '''Slide Number 8'''

'''Summary'''
| | In this tutorial we learnt to :

* Import molecules from the database

* Rotate, zoom in and zoom out

* Build molecules on the panel

* Set up force field and optimize geometry

* Measure bond lengths, bond angles, dihedral angles

* Show fragment library

* Build DNA molecules and peptides.
|-
| | '''Slide Number 9'''

'''Assignment 1'''
|| As an assignment

* Create a protein sequence using the following amino acid residues:

'''Glu, Leu, Asn, Cys, His'''.

* Optimize the geometry using '''UFF''' force field

* Save the image as '''.cml''' file.
|-
|| '''Slide Number 10'''

'''Assignment 2'''
|| Assignment:

* Build '''RNA''' sequence using the Nucleic acids: '''AUGC'''

* Optimize geometry using '''MMFF94''' force field

* Save the image as '''.cml''' file.
|-
|| '''Slide Number 11'''

'''Acknowledgement '''

Watch the video available at

http://spoken-tutorial.org/What is a Spoken Tutorial

It summarises the Spoken Tutorial project.

If you do not have good bandwidth, you can download and watch it.
||
* This video summarizes the Spoken Tutorial project

* If you do not have good bandwidth, you can download and watch it.
|-
| | '''Slide Number 12'''

The Spoken Tutorial Project Team,

Conducts workshops using spoken

tutorials

Gives certificates to those who pass an online test

For more details, please write to,

'''contact@spoken-tutorial.org'''
|| * We conduct workshops using Spoken Tutorials and give certificates.

* Please contact us.
|-
|| '''Slide number 13'''

Spoken Tutorial Project is a part of the Talk to a Teacher project

It is supported by the National Mission on Education through ICT, MHRD, Government of India

More information on this Mission is available at:

'''http://spoken-tutorial.org/NMEICT-Intro '''
|| Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India
|-
||
|| This tutorial is contributed by Viswa Janani Vasudhevan and Madhuri Ganapathi. Thank you for joining.
|-
|}

@@ Line 27: / Line 27: @@
 * Show fragment library
-* Build DNA molecules and peptides.
+* Build DNA molecules and '''Peptides'''.
 |-
 || '''Slide Number 3'''
@@ Line 34: / Line 34: @@
 || 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
 * Working Internet connection.
@@ Line 58: / Line 58: @@
 '''sourceforge.net/projects/avogadro'''.
-I have already downloaded Avogadro.
+I have already downloaded '''Avogadro'''.
 |-
 || Click on''' Dash home.'''
@@ Line 66: / Line 66: @@
 |-
 || Cursor on the '''Avogadro''' icon.
-|| Click on '''Avogadro''' icon to open the application window.
+|| Click on '''Avogadro''' icon to open the application.
 |-
 ||
@@ Line 140: / Line 140: @@
 Click on '''Other''' see the '''Periodic table'''.
-Click on close(X).
+Click on '''Close'''(X).
 || '''Element''' drop down list shows list of elements.
 Click on '''Other''' to view the entire '''Periodic table''' in a separate window.
-Click on close(X) to close the window.
+Click on '''Close'''(X) to close the window.
 |-
 || Cursor on the Panel.
@@ Line 208: / Line 208: @@
 It will take a few seconds to complete the optimization.
-Click on '''Stop''' to close the ''' AutoOptimization Settings'''.
+Click on '''Stop''' to close the ''' Optimization Settings'''.
 |-
 || Cursor on the Panel
@@ Line 224: / Line 224: @@
 || Select '''Click to Measure''' icon on the tool bar.
-To measure distance click on any two consecutive carbon atoms.
+To measure distance, click on any two consecutive carbon atoms.
 To measure angles, click on any 3 consecutive atoms.
@@ Line 235: / Line 235: @@
 || To save the file, click on '''File''' and '''Save As'''.
 |-
-|| Point to the dialogue box.
+|| Point to the dialog box.
 || '''Save Molecule As''' dialog box appears.
 |-
@@ Line 263: / Line 263: @@
 |-
 || Point to the list of folders.
-|| we can see list of folders having '''cml''' files of different chemical structures.
+|| We can see list of folders having '''cml''' files of different chemical structures.
 |-
 || Double click on the folder to see '''.cml''' files.
@@ Line 279: / Line 279: @@
 Click on '''Insert''' button.
-Click on close to close the dialog box.
+Click on '''Close''' to close the dialog box.
 |-
 || Point to the structure.
@@ Line 289: / Line 289: @@
 |-
 || Press '''CTRL+SHIFT+A'''.
-|| The molecule is in select mode, to de-select
+|| The molecule is in select mode.
-Press '''CTRL''', '''SHIFT''' and '''A''' keys simultaneously.
+To de-select, press '''CTRL''', '''SHIFT''' and '''A''' keys simultaneously.
 |-
 || Show the images of '''Vitamin A''' and '''natural rubber.'''
@@ Line 309: / Line 310: @@
 || Click on '''Build''' menu, navigate to '''Insert''' and select '''Fragment.'''
-Scroll down to '''macrocycles''' folder, double click to open.
+Scroll down to '''macrocycles''' folder; double click to open.
 |-
 || Select '''porphin''' fragment.
@@ Line 318: / Line 319: @@
 |-
 || Show structure of '''chlorophyl''' molecule and '''Vitamin B12''' molecules.
-|| Using '''porphyrin''' fragment we can build complex chemical structures:
+|| Using '''porphyrin''' fragment, we can build complex chemical structures:
 Such as '''Chlorophyll''' and '''Vitamin B12'''.
@@ Line 338: / Line 339: @@
 || To insert a '''DNA''' molecule, go to '''Build''' menu navigate to '''Insert'''
-Select '''DNA/RNA''' from the sub-menu.
+And click on '''DNA/RNA''' from the sub-menu.
 |-
 || Point to the box.
@@ Line 352: / Line 353: @@
 |-
 || Point to the molecule.
-|| You can choose your own sequence of '''nucleic acids'''.
+|| You can choose your own sequence of '''acids'''.
-For demonstration I will select '''ATGC ATGC'''.
+For demonstration I will select '''A T G C A T G C'''.
 The order of selection of '''nucleic acids''' appear in the '''Sequence''' text box.
@@ Line 365: / Line 366: @@
 Select '''Strands''' as '''Single''' and click on '''Insert''' button.
 |-
-|| Click on close(X) to close the dialog box.
+|| Click on Close(X) to close the dialog box.
-|| Click on close(X) to close the dialog box.
+|| Click on '''Close'''(X) to close the dialog box.
 |-
 || Point to the molecule.
-|| We now have a single stranded '''DNA''' molecule on '''Panel'''.
+|| We now have a single stranded '''DNA''' molecule on the '''Panel'''.
 Zoom out the structure and drag to the centre of the '''Panel'''.
 |-
 || press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
-|| To deselect the''' DNA''' molecule on Panel,
+|| To deselect the''' DNA''' molecule on the '''Panel''',
 press '''CTRL, Shift''' and '''A''' keys simultaneously.
@@ Line 390: / Line 391: @@
 |-
 || Select '''amino acid''' sequence as Gly-Val-Pro-Cys, click on '''Insert Peptide''' button.
-|| Select '''amino acids''' for the '''peptide''' sequence by clicking on the '''amino acids''' buttons.
+|| Select '''amino acids''' for the '''Peptide''' sequence by clicking on the '''amino acids''' buttons.
 For demonstration I will choose the sequence as '''Glycine(Gly)''' -'''Valine(Val)''' -'''Proline(Pro)''' and '''Cystine(Cys)'''.
@@ Line 405: / Line 406: @@
 || Point to the '''Peptide '''chain.
-To de-select the '''Peptide''' on '''Panel''',
+To de-select the '''Peptide''' on '''Panel''', press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
-−
 press '''CTRL''', '''Shift''' and '''A''' keys simultaneously.
 || '''Peptide''' chain appears on the '''Panel'''.
@@ Line 436: / Line 435: @@
 * Show fragment library
-* Build DNA molecules and peptides.
+* Build '''DNA''' molecules and '''Peptides'''.
 |-
 | | '''Slide Number 9'''
@@ Line 456: / Line 455: @@
 || Assignment:
-* Build '''RNA''' sequence using the Nucleic acids: '''AUGC'''
+* Build '''RNA''' sequence using the '''Nucleic acids: AUGC'''
 * Optimize geometry using '''MMFF94''' force field