Jmol-Application/C4/3D-Models-of-Enzymes/English - Revision history

PoojaMoolya at 09:53, 28 October 2020

2020-10-28T09:53:58Z

2015-01-07T06:29:43Z

2015-01-07T06:22:26Z

2015-01-07T06:19:11Z

2015-01-07T06:16:54Z

2015-01-07T06:05:53Z

2015-01-07T06:03:36Z

2015-01-07T06:02:37Z

2015-01-07T05:52:04Z

2015-01-07T05:50:17Z

@@ Line 51: / Line 51: @@
 ||Cursor on input box.
 Type '''3IDH''' in the text box.
-||An Input dialogue box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.
+||An Input dialog box appears on the screen. Type the four letter '''PDB code''' for '''hexokinase''',  that is '''3IDH'''  in the text box.
 |-
 ||Cursor on the Jmol panel

@@ Line 180: / Line 180: @@
 ||Cursor on the panel.
 ||As mentioned earlier the amino acids involved at the active-site are
 '''Aspergine''' at position 204
-'''Aspergine''' at position 231 and
+'''Aspergine''' at position 204
 '''Glutamic acid''' at 256
 |-
 ||Open the file menu, scroll down to '''Console''' and click on it.
@@ Line 246: / Line 249: @@
 ||'''Slide Number 9
 Summary'''
-||* Highlight substrate and cofactors of the enzyme.
+||
 * And View '''ramachandran''' plot for  proteins.
 |-
@@ Line 258: / Line 262: @@
 * Highlight the amino acids at the active site.
-Hint: Get the '''pdb file''' of ''Lysozyme'''  from  '''PDB database'''.
+Hint: Get the '''pdb''' file of '''Lysozyme'''  from  '''PDB database'''.
 |-
 ||'''Slide Number11

@@ Line 191: / Line 191: @@
 Press enter key on the keyboard.
 ||At the $ prompt type:
-select within square brackets Asn for '''aspergine'' close the bracket, 204 i.e the position semicolon color atoms orange.
+'''select within square brackets Asn for aspergine close the bracket, 204 i.e the position semicolon color atoms orange'''.
 Press enter.
 |-

@@ Line 150: / Line 150: @@
 |-
 ||Open pop-up menu, Scroll down to '''Color''', go to '''Atoms''', click on '''Blue''' option.
-||Open the pop-up menu again, go to '''Color''', '''Atoms''', click on '''Blue''' option.
+||Open the pop-up menu again, go to '''Color''', '''Atoms''', and click on '''Blue''' option.
 |-
 ||Cursor on the panel

@@ Line 92: / Line 92: @@
 Hexokinase'''
 || Active-site  for '''hexokinase''' has 3 amino acid residues:
-* Aspergine at 204,
+* '''Aspergine''' at 204,
-* Aspergine at position 231 and
+* '''Aspergine''' at position 231 and
-* Glutamic acid at 256.
+* '''Glutamic acid''' at 256.
 '''Alpha-D-Glucose''' is the substrate for this enzyme.
@@ Line 129: / Line 129: @@
 |-
 ||Exit the pop-up menu.
-||We can modify the display of the enzyme to easily locate the substrate binding site.`
+||We can modify the display of enzyme to easily locate the substrate binding site.`
 |-
 ||Cursor on the panel.
-||Let us change the display and color of the atoms of protein.
+||Let us change the display and color of the atoms of the protein.
 |-
 ||Open the pop-up menu.
@@ Line 140: / Line 140: @@
 Click on '''All'''.
 |-
-||Open the Pop-up menu again, go to '''Style''', then to '''Scheme'''.
+||Open the Pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.
 Click on '''Sticks''' option.
 ||Open the pop-up menu again, scroll down to '''Style''', then to '''Scheme'''.

@@ Line 99: / Line 99: @@
 |-
 ||Cursor on Jmol panel.
-||Let us now go back to the Jmol panel.
+||Now let us go back to the Jmol panel.
 |-
 ||Cursor on Jmol panel with the model of '''hexokinase'''

@@ Line 17: / Line 17: @@
 ||'''Slide Number 3
 Learning Objectives'''
-||*
+||
 * Highlight substrate and cofactors of the enzyme.
 * And view '''Ramachandran plot''' for protein

@@ Line 17: / Line 17: @@
 ||'''Slide Number 3
 Learning Objectives'''
-|| In this tutorial, we will learn to
+||*
 * Highlight substrate and cofactors of the enzyme.
 * And view '''Ramachandran plot''' for protein
@@ Line 70: / Line 70: @@
 ||Cursor on the Console.
 ||As shown on the Console:
 The structure on the panel  is for '''Human Pancreatic Glucokinase''' along with substrate '''Glucose'''.
 Close the Console.
@@ Line 79: / Line 80: @@
 ||Remove the '''water molecules''' from the '''protein model''' on the panel.
-This process is explained in detail in the  Jmol tutorial Proteins and macromolecules.
+This process is explained in detail in the  Jmol tutorial '''Proteins and macromolecules'''.
 |-
 ||'''Slide Number 6'''

@@ Line 27: / Line 27: @@
 And familiar with  basic operations from  '''Jmol Application window'''.
-Please view  the tutorial ''Proteins and Macromolecules' in the Jmol Application series.
+Please view  the tutorial '''Proteins and Macromolecules''' in the Jmol Application series.
 It is available at the following link.

@@ Line 29: / Line 29: @@
 Please view  the tutorial ''Proteins and Macromolecules' in the Jmol Application series.
-Macromolecules' in the Jmol Application series
+It is available at the following link.
 |-
 ||'''Slide Number 5
 System Requirement'''
 ||To record this tutorial I am using,
-* '''Ubuntu Linux''' OS version 12.04 .
+* '''Ubuntu''' Operating System version 12.04 .
 * '''Jmol''' version 12.2.2.
 * '''Java''' version 7. and
@@ Line 131: / Line 131: @@
 |-
 ||Cursor on the panel.
-||Let us change the display and color of the atoms of the protein.
+||Let us change the display and color of the atoms of protein.
 |-
 ||Open the pop-up menu.