Difference between revisions of "Jmol-Application/C2/Proteins-and-Macromolecules/English-timed"

| In this tutorial, we will learn to

|* Load structures of proteins from '''Protein Data Bank (PDB).'''

|* Download '''.pdb '''files from '''PDB''' database.

| To follow this tutorial you should be familiar with basic operations from '''Jmol Application window.'''

|To record this tutorial I am using,

|Structure Analysis of large '''biomolecules''' such as  

|Here I have opened a new '''Jmol''' window.

|3D structures of '''biomolecules''' can be viewed, by direct download from database.  

| An input dialog box appears on screen.  

| This code can be obtained from the '''Protein Data Bank (PDB) '''website'''.'''

| This is the web page of '''Protein Data Bank.'''

| In the search box type name of the protein as '''Human''' '''Insulin.'''Press Enter key on the keyboard.

| Information like  

| We can save the structures of proteins as '''.pdb '''files and view them in 3D mode in '''Jmol.'''

| Click on the '''Download Files''' link, located at the top right hand corner of the page.  

| From the drop down menu, select '''PDB file (gz) '''option'''. '''

| The structure of protein will be saved as '''4EX1.pdb.gz,''' in the '''Downloads '''folder.

| Similarly, you can download the required '''.pdb '''files of various proteins and save them in separate files.  

| Now, lets switch to '''Jmol''' window to view the 3D structure of '''Insulin'''.

| If you are connected to Internet, you can directly download the protein structure on Jmol panel.

|Select '''Downloads''' folder and click on '''open '''button.  

|Select '''4EX1.pdb.gz''' file and click on '''open''' button.

| The default display of the '''protein''' on the panel, is '''ball and stick.'''

| The model of protein on the panel is shown without hydrogens atoms.

| From the sub-menu,choose '''Hetero'''and click on '''“All Water''' option.

| Open the pop-up menu again and go to '''Style''' scroll down to '''Atoms '''and click on '''Off '''option.

| Now on panel we have '''Insulin'''structure without any water molecules.

|A sub-menu opens with options like '''CPK Spacefill''', '''Ball and Stick, Sticks, Wireframe, cartoon, trace, etc. '''

| To change the color of display, open the Pop-up-menu. Scroll down to '''Color''' select '''Atoms''' and click on '''Blue''' option.

| We can also highlight '''hydrogen bonds '''and''' di-sulpfide bonds '''in the protein model.

|'''Calculate''', '''Set Hydrogen Bonds Side Chain.'''

|'''Set Hydrogen Bonds in the Backbone.'''

And also has options to change the thickness of the bonds.

| To change the thickness of '''hydrogen bonds''', Click on''' 0.10 A '''option from the''' pop-up-menu'''.

|Now on the panel we can see thicker''' hydrogen bonds'''.  

| From the Pop-up-menu scroll down to '''Color''' then '''Hydrogen Bonds''' then click on '''orange''' option.

|   '''Disulfide''' bonds, and sulphur atoms are shown in the model in yellow colour.

| To modify disulfide bonds open the option disulfide bonds in pop menu

| Click on the features you may want to change like size and color etc.

| Similarly try to open '''.pdb '''files of different '''enzymes '''and view their 3D structures.

| Let us summarize, in this tutorial we have learnt to:

|* To Load structures of protein from Protein Data Bank (PDB).

|* Download '''.pdb''' files from the database.

| Here is an assignment for you.

|* Download the '''.pdb''' file of '''Human Hemoglobin''' from '''PDB '''database.

[http://spoken-tutorial.org/What http://spoken-tutorial.org/What]_is_a_Spoken_ Tutorial

|It summarizes the Spoken Tutorial project

|If you do not have good bandwidth, you can download and watch it  

| The Spoken Tutorial Project Team:  

|Conducts workshops using spoken tutorials

|Gives certificates to those who pass an on-line test  

|For more details, please write to  contact@spoken-tutorial.org  

| 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 this link [http://spoken-tutorial.org/NMEICT-Intro http://spoken-tutorial.org/NMEICT-Intro] ]

|This is Snehalatha from IIT Bombay signing off. Thank you for joining.