Difference between revisions of "UCSF-Chimera/C4/Attributes/English"

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Line 60: Line 60:
  
 
Press enter.
 
Press enter.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I have opened the '''Chimera''' window.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Here I have opened a '''Chimera''' window.
  
  
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Press enter
 
Press enter
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Change the display to sticks, type,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To change the display to sticks, type,
  
  
 
'''rep stick'''
 
'''rep stick'''
 +
 +
Press enter
  
  
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Click on “a'''ttributes'''” button on the right side of the panel.
 
Click on “a'''ttributes'''” button on the right side of the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''Model Panel''' dialog box appears on the screen.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Model Panel''' dialog box appears on the screen.
  
  
Line 161: Line 163:
  
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| A '''Attributes''' dialog box for '''1zik''' opens on the screen.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|'''Attributes''' dialog box for '''1zik''' opens on the screen.
  
  
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'''rep bs'''
 
'''rep bs'''
  
−
Press enter.
+
 
  
 
|-
 
|-
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| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now click on '''Component Bond Attributes.'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now click on '''Component Bond Attributes.'''
  
−
Here there are options to change bond style.
+
Here, there are options to change bond style to '''stick''' or '''wire'''.
  
 
|-
 
|-
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Close the '''color editor''' dialog box.
 
Close the '''color editor''' dialog box.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, In the '''Attribute '''dialog box,
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Now, click in the '''Attribute '''dialog box,
  
−
Click on the '''color well '''next to '''ribbon color'''.  
+
Now,in the attribute dialog-box, click on the '''color well '''next to '''ribbon color'''.  
  
 
Select a ribbon color, and click on close option to close the '''color editor'''.
 
Select a ribbon color, and click on close option to close the '''color editor'''.
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|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Scroll down the Tools menu, select '''Structure Analysis '''option.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on  '''Tools''' menu, scroll down to  '''Structure Analysis '''.
  
 
From the sub-menu select '''Render by Attribute.'''
 
From the sub-menu select '''Render by Attribute.'''
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the the '''Attribute''' list.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on the the '''Attribute''' list.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Attribute''' list to check for the available options.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Attribute''' list to check for available options.
  
  
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−
 
+
Back to the panel.
  
 
|-
 
|-
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−
Click on '''colors''' option.
+
Click on '''colors''' button.
  
 
Click on '''color atoms, keep opaque '''and''' color surfaces.'''
 
Click on '''color atoms, keep opaque '''and''' color surfaces.'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| There are 3 options to display the structure according to '''B-factor''' value; '''colors''', '''radii '''or '''worms'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"|Check options for '''color atoms''', '''keep opaque''' and '''color surfaces.'''
−
 
+
−
Click on '''Colors'''.
+
−
 
+
−
Check options for '''color atoms''', '''keep opaque''' and '''color surfaces.'''
+
  
 
The default color '''palette''' is blue and red.
 
The default color '''palette''' is blue and red.
  
−
You can change the color '''palette''', if you wish to change the colors.  
+
You can change the color '''palette''', using drop-down menu.  
  
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click '''Apply.'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click '''Apply.'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click '''Apply''' button.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Apply''' button.  
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As expected atoms with higher '''B-factors''' are on the outside of the structure.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| As expected atoms with high '''B-factors''' are on the outside of the structure.  
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select '''residues '''in the''' attributes drop-down''' in the''' Render dialog box.'''
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select '''residues '''in the''' attributes drop-down''' in the''' Render dialog box.'''
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the '''Attribute''' '''dialog box''', click on '''Attributes button.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| In the '''Select by Attribute''' '''dialog box''', click on '''Attributes button.'''
  
 
From the drop-down, select '''residues'''.
 
From the drop-down, select '''residues'''.
Line 469: Line 467:
 
|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Select '''Render.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Render.'''
  
 
The '''attributes''' for residues include '''kdHydrophobicity scale'''.
 
The '''attributes''' for residues include '''kdHydrophobicity scale'''.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Select '''kdHydrophobicity .'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''kdHydrophobicity ''' from the drop-down menu.
  
  
  
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Select '''kdHydrophobicity from the drop-down menu.'''
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''kdHydrophobicity from the drop-down menu.'''
  
  
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Cursor on the panel.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Hydrophobicity''' of the residues can be shown with colors or with worms.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| '''Hydrophobicity''' of the residues can be shown with colors or worms.  
  
  
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−
The '''hydrophobic '''residues are colored in red, and hydrophilic residues are colored in blue.
+
The '''hydrophobic''' residues are colored in red, and polar residues are colored in blue.
  
 
|-
 
|-
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Worms''' option.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''Worms''' button.
  
  
 
Click on '''apply'''.
 
Click on '''apply'''.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Worms''', Click on '''Apply'''.
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Click on '''Worms''' button, Click on '''Apply'''.
  
 
Observe the panel.
 
Observe the panel.
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−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| The most '''hydrophobic''' residues face the interior of the structure.  
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| Most '''hydrophobic''' residues face the interior of the structure.  
  
 
|-
 
|-
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|-
 
|-
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''worm style''' to '''non-worm'''. Click on '''OK'''.
 
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:none;padding:0.097cm;"| Click on '''worm style''' to '''non-worm'''. Click on '''OK'''.
−
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To return to normal '''ribbon''' instead of '''worm'''<nowiki>;</nowiki>
+
| style="background-color:#ffffff;border-top:none;border-bottom:1pt solid #000000;border-left:1pt solid #000000;border-right:1pt solid #000000;padding:0.097cm;"| To return the structure to normal '''ribbon'''<nowiki>;</nowiki>
  
−
Click on the worm-style button and choose '''non-worm'''. Click on '''OK '''button'''.'''
+
Click on worm-style button and choose '''non-worm''' option. Click on '''OK '''button'''.'''
  
 
|-
 
|-
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−
* Color the residues according to the '''kdHydrophobicity '''values.
+
* Color the residues according to '''kdHydrophobicity '''values.
  
 
|-
 
|-

Revision as of 17:52, 2 September 2016

Visual Cue
Narration
Slide Number 1

Title Slide

Welcome to this tutorial on Attributes.



Slide Number 2

Learning Objectives

In this tutorial we will learn to,


  • Change attributes of atoms, residues and models.


  • Color atoms in a protein according to B-factor values.


  • Color residues according to kdhydrophobicity values.
Slide Number 3

Pre-requisites

To follow this tutorial you should be familiar with,


Chimera interface

If not, for relevant tutorials, please visit our website.

Slide Number 4

System Requirement

To record this tutorial I am using

Ubuntu OS version. 14.04

Chimera version 1.10.2

Mozilla Firefox browser 42.0

And a working Internet connection.

Double-click on the Chimera icon present on the desk top.


Type, open 1zik


Press enter.

Here I have opened a Chimera window.


Using command line open the structure of Leucine zipper.


On the command text box, type, open 1zik


Press enter.

Cursor on the panel.


Click on Presets menu, click on Interactive 2.

The model on the panel is shown as ribbons.


Using Presets menu, change the display to Interactive 2 .

On the command line type,

delete solvent.


Press enter.

To hide water molecules, on the command line type,

delete solvent.


Press enter.

On the command line type,

rep sticks


Press enter

To change the display to sticks, type,


rep stick

Press enter



On the command line type,


addh , Press enter.

Add hydrogens to the structure, type,

addh

Cursor on the panel. Now let us learn how to change the attributes of atoms and residues for this structure.
Slide Number 5

Attributes

  • Attributes are properties with names and values.
  • In Chimera, items such as atoms, bonds, residues and molecule models have Attributes.
Cursor on the panel. There are different ways to change the Attributes.
Click on the Favorites menu, scroll down and click on Model Panel. Open the Model Panel using Favorites menu.
Cursor on the Model Panel dialog box.


Click on “attributes” button on the right side of the panel.

Model Panel dialog box appears on the screen.


Click on the attributes button on the right side of the panel.



Cursor on the 1zik Attributes dialog box.

Click on Molecule Attributes button.


Attributes dialog box for 1zik opens on the screen.


The dialog box has attribute list.



Cursor on the panel.


Click on Molecule Attributes

The list includes.

Molecule Attributes and its components, Atom, bond and residue attributes.


Select Molecule Attributes.

Cursor on the dialog box.

Click on Molecule Attributes.

The available attributes are listed on the window.
click on aromatic display button.


Select True from the drop-down menu.

For example to change the display of aromatic rings;


Click on the button next to aromatic display.


Select True from the drop-down.

Click on Disk in the Aromatic ring style option.


Select Aromatic ring style as disk.

Click on the color well next to aromatic color.

Select color from the color editor.

Close the dialog box.

Zoom the structure.

Cursor on Aromatic rings.

Observe the panel.

All the aromatic rings are shown with disks in the center.

Type,

rep bs

Press enter.

Change the display of the structure to ball and stick.


On the command line, type,

rep bs


Change the ball scale value to 0.5.


On the attributes dialog box, change the Van der Walls radii of the atoms.

Change the value of ball scale to 0.5.

press enter.



Cursor on the panel. Observe the panel. The atoms are shown with larger atomic radii.
Click on Atom Attributes. Again click on Molecular Attributes check box.

From the list, click on Component Atom Attributes.



Select sphere. In the corresponding window, click on atom style button .

The drop-down menu has many options.

Click on sphere to change the display to cpk.

Observe the panel.

Select dot to bring back the sticks display.

Click on Component Bond Attributes. Now click on Component Bond Attributes.

Here, there are options to change bond style to stick or wire.

Click on Component Residue Attributes. Click on Component Residue Attributes.

Here we have options to change the attributes of the ribbon.



Click on Presets menu, change the display to ribbons. Using presets menu, change the display of the structure on the panel to ribbons.
Click on the color well.

Choose a color from the color editor dialog box.

Close the color editor dialog box.

Now, click in the Attribute dialog box,

Now,in the attribute dialog-box, click on the color well next to ribbon color.

Select a ribbon color, and click on close option to close the color editor.



Click on ribbon cross-section select edged from the options.


There are options to change the cross-section of the ribbon and scaling.


Close the dialog box.

Click on Presets menu, select Interactive 2 option. Again change the display to atoms using Presets menu.
Cursor on Tools menu. Attributes can also be changed using Tools menu.
Click on Tools menu, scroll down to Structure Analysis .

From the sub-menu select Render by Attribute.

Click on tools menu, scroll down to Structure Analysis.

And select Render by Attribute option from the sub-menu.

Cursor on the dialog box.


A Render by attribute dialog box opens.



Cursor on Render by attribute dialog box.


Click on atoms from the Attributes drop-down.

Here we have options to change the attributes of atoms, residues, molecules, segmentation regions etc.

Select atoms.


Click on Render.

Click on the the Attribute list. Click on Attribute list to check for available options.


The list shows two options;


bfactor and occupancy


These two attributes can be read from the input PDB file.

Select bfactor.


Cursor on the Histogram.

Choose bfactor.


A histogram of values will appear, with colored vertical bars.

Slide Number 6

B-factor

  • B-factor values are a measure of mobility in the macromolecule.
  • Atoms with low B-factor values belong to a part of the structure that is well ordered.
  • Atoms with large B-factor values belong to part of the structure that is very flexible.
Slide Number 7

B-factor

PDB file for a protein structure contains B-factor information.


Back to the panel.

Drag the vertical bars on histogram using mouse.


Cursor on the Value text box.


Drag the blue vertical bar to zero, red to 100.

Fix the white bar at value 50.

Back to the panel.


The vertical bars can be dragged along the histogram with the mouse.

The Value of B-factor is displayed in the Value text box.


Drag the blue vertical bar to zero, red to 100.

Then fix the white bar at value 50.

Cursor on the panel.


Click on colors button.

Click on color atoms, keep opaque and color surfaces.

Check options for color atoms, keep opaque and color surfaces.

The default color palette is blue and red.

You can change the color palette, using drop-down menu.

Click Apply. Click on Apply button.
Cursor on the panel.


Observe the panel.

Atoms with high B-factor values are shown in red and least in blue.

Cursor on the panel. As expected atoms with high B-factors are on the outside of the structure.
Cursor on the panel. Now let us change the attributes of Residues.
Select residues in the attributes drop-down in the Render dialog box. In the Select by Attribute dialog box, click on Attributes button.

From the drop-down, select residues.

Cursor on the panel. Click on Render.

The attributes for residues include kdHydrophobicity scale.

Click on kdHydrophobicity from the drop-down menu.


Click on kdHydrophobicity from the drop-down menu.


The values are displayed in the histogram.

Slide Number 8

kdHydrophobicity

  • kdHydrophobicity scales are values that define relative hydrophobicity of amino acid residues.


  • KdHydrophobicity values are positive for hydrophobic residues and Negative values for polar residues.
Cursor on the panel. Hydrophobicity of the residues can be shown with colors or worms.


Choose Colors. By default some of the parameters are selected.


Click on Apply button. observe the panel.


The hydrophobic residues are colored in red, and polar residues are colored in blue.

Click on Worms button.


Click on apply.

Click on Worms button, Click on Apply.

Observe the panel.

Worms are modified ribbons that vary in radius.

Cursor on the panel.


Most hydrophobic residues face the interior of the structure.
Cursor on the panel. By default, the more hydrophobic residues will be shown with larger radius.
Click on worm style to non-worm. Click on OK. To return the structure to normal ribbon;

Click on worm-style button and choose non-worm option. Click on OK button.

Click on File menu, scroll down and click on Close Session option. Close the Chimera session using File menu.



Slide Number 9

Summary

Let's summarize,

In this tutorial we have learnt to,


  • Change attributes of atoms, residues and models.


  • Color atoms in a protein according to B-factor values.


  • Color residues according to kdHydrophobicity values.



Slide Number 10

Assignment

As an Assignment,


  • Open a model of hemoglobin (PDB code: 2HCO) on the panel.


  • Color the atoms according to B-factor values.


  • Color the residues according to kdHydrophobicity values.
Slide Number 11

Acknowledgement

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


Slide Number 12 * We conduct workshops using Spoken Tutorials and give certificates.
  • Please contact us.


Slide number 13 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
This is Snehalatha from IIT Bombay signing off.

Thank you for joining.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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