Difference between revisions of "UCSF-Chimera/C2/Picking-and-Selection/English-timed"

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|  00:01
 
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|  Welcome to this tutorial on '''Picking and Selection '''using Chimera.
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|  Welcome to this tutorial on '''Picking and Selection '''using '''Chimera'''.
  
 
|-
 
|-
 
|  00:06
 
|  00:06
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|  In this tutorial, we will learn to  Show labels for atoms and '''residues'''.
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|  In this tutorial, we will learn to: show labels for atoms and '''residues''',
  
 
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|  00:12
 
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|  Select '''atoms''' and '''residues''' using '''Select menu''' or by '''Picking'''.
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|  select atoms and '''residues''' using '''Select menu''' or by '''Picking''',
  
 
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|  00:17
 
|  00:17
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|  Change the color and display of the '''residues'''.
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|  change the color and display of the '''residues''',
  
 
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|  00:21
 
|  00:21
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|  Add, delete or change atoms ,  Rotate bonds
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|  add, delete or change atoms ,  rotate bonds,
  
 
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|  00:27
 
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|  Open more than one model on the display window. Select and move the model.
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|  open more than one model on the display window, select and move the model.
  
 
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| 00:34
 
| 00:34
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|  To follow this tutorial you should have knowledge of  Undergraduate '''Biochemistry'''.
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|  To follow this tutorial, you should have knowledge of  undergraduate Biochemistry.
  
 
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| 00:40
 
| 00:40
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| Or familiar with '''structural biology'''. For relevant tutorials, please visit our website.  
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| Or familiar with '''structural biology'''. For relevant tutorials, please visit our '''website'''.  
  
 
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|  00:47
 
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|  To record this tutorial, I am using, '''Ubuntu Operating System''' version. 14.04
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|  To record this tutorial, I am using: '''Ubuntu Operating System''' version 14.04,
  
 
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|  00:52
 
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| '''Chimera''' version 1.10.2
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| '''Chimera''' version 1.10.2,
  
 
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| '''Mozilla firefox''' browser 35.0
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| '''Mozilla firefox''' browser 35.0,
  
 
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| And a working internet connection.
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| and a working internet connection.
  
 
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|  Individual components of the structure such as: residues, atoms, bonds etc can be modified using tools available in '''Chimera'''.
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|  Individual components of the structure such as: '''residue'''s, atoms, '''bond'''s etc. can be modified using tools available in '''Chimera'''.
  
 
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|  There are different ways to make a selection:  using the '''Select''' menu in the menu bar.
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|  There are different ways to make a selection:  using the '''Select''' menu in the menu bar,
  
 
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|  01:40
 
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|  '''Picking''' from the '''graphics''' window.
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|  '''Picking''' from the '''graphics''' window,
  
 
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| 01:43
 
| 01:43
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|  Typing commands on the command line. Or by selecting, '''Model Panel''' and '''Sequence''' option present in the '''Favorites''' menu.
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|  typing '''command'''s on the '''command line''', Or by selecting '''Model Panel''' and '''Sequence''' option present in the '''Favorites''' menu.
  
 
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|  01:53
 
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|  Back to the Chimera window.
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|  Back to the '''Chimera window'''.
  
 
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| 01:55
 
| 01:55
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| '''Leucine zipper''' motif consists of periodic repetition of '''leucine''' residues.  
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| '''Leucine zipper motif''' consists of periodic repetition of '''leucine''' residues.  
  
 
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Revision as of 20:15, 25 June 2018

Time
Narration
00:01 Welcome to this tutorial on Picking and Selection using Chimera.
00:06 In this tutorial, we will learn to: show labels for atoms and residues,
00:12 select atoms and residues using Select menu or by Picking,
00:17 change the color and display of the residues,
00:21 add, delete or change atoms , rotate bonds,
00:27 open more than one model on the display window, select and move the model.
00:34 To follow this tutorial, you should have knowledge of undergraduate Biochemistry.
00:40 Or familiar with structural biology. For relevant tutorials, please visit our website.
00:47 To record this tutorial, I am using: Ubuntu Operating System version 14.04,
00:52 Chimera version 1.10.2,
00:57 Mozilla firefox browser 35.0,
01:01 and a working internet connection.
01:04 Here I have opened a Chimera window.
01:07 On the rapid access window, click on 1zik from the list of recently accessed data.
01:15 A model of Leucine zipper opens on the graphics window.
01:20 Individual components of the structure such as: residues, atoms, bonds etc. can be modified using tools available in Chimera.
01:31 The first step is to make selection.
01:34 There are different ways to make a selection: using the Select menu in the menu bar,
01:40 Picking from the graphics window,
01:43 typing commands on the command line, Or by selecting Model Panel and Sequence option present in the Favorites menu.
01:53 Back to the Chimera window.
01:55 Leucine zipper motif consists of periodic repetition of leucine residues.
02:02 I will now demonstrate how to highlight the leucine residues present in this structure.
02:08 From the presets menu choose interactive 2 option.
02:12 This will convert the structure to atoms display. From the Select menu choose Residue option.
02:20 The sub-menu has many options.
02:23 The Amino acid category menu has amino acids grouped as: aliphatic, aromatic, hydrophobic, polar etc.
02:34 Standard amino acid menu has list of amino acid residues present in the structure.

Click on leucine.

02:42 All the leucine residues are now highlighted.
02:46 Click on actions menu, select color.
02:49 I will choose yellow from the list of colors. All the leucines are now displayed in yellow color.
02:57 To clear the selection, click on Select menu. Then click on Clear selection option.
03:03 Leucine being hydrophobic is packed into the hydrophobic core of the protein.
03:09 Now change the display to ribbons using presets option. Click on Interactive 1.
03:17 To pick a residue from the screen : Hover the cursor over the structure.
03:22 A pop-up balloon appears with identifying information.
03:26 It has information such as residue name, residue number and Chain.
03:32 The balloon disappears when you move the cursor.
03:36 Bring the cursor to the first residue on chain A, that is arginine.
03:41 Press and hold the CTRL key on the keyboard and click the left mouse button.

Release the CTRL key.

03:49 The outline of the residue is highlighted. By default the selection is outlined in green.
03:57 If you want to select more than one residue; Press and hold both CTRL and shift key on the key board.
04:04 Hover the mouse over the peptide chain. Click on the residues you want to pick.
04:10 Release the CTRL and Shift keys from the keyboard.
04:14 Now you have picked the residues for modification.
04:18 Choose an option from the Actions menu. Click on Actions menu.
04:23 For example to display atoms, choose atoms/bonds.

Click on Show.

04:30 The selected residues are now seen in atoms display. Clear the selection.
04:36 We can also modify atoms or bonds present in the structure by Picking.
04:42 Place the cursor over an object such as an atom, or bond.
04:47 This will show its label information in an atomspec balloon.
04:52 Atomspec balloon for an atom has information such as: Residue name, number, chain and atom name.
05:01 To select an atom, press and hold the CTRL key on the keyboard.
05:06 While holding the CTRL key click on the atom you want to change.
05:11 The atom is now highlighted. To modify the atom double-click on the atom while holding the CTRL key.
05:20 A context menu opens with options.
05:24 Click on Modify-atom option. Release the CTRL key.
05:30 A Build Structure window opens.
05:33 Let us change the selected atom that is Nitrogen to a methyl group.
05:38 The Build Structure window, Select element as carbon, bonds as 4 and Click on apply button.
05:49 Observe the panel.
05:51 A methyl group is now added to the existing structure.

Close the window.

05:57 There is also an option to rotate bonds.
06:00 Hover the cursor over the bond you want to rotate.
06:04 Information regarding the bond appears in the atomspec balloon.
06:09 To select a bond, place the cursor on the bond.
06:13 Press and hold the CTRL key. Click the left mouse button.
06:18 The selected bond is now highlighted. While still holding the CTRL key double click on the bond.
06:26 Release the CTRL key on the key board.
06:29 A context-menu opens. Click on rotate bond option.
06:35 A Build Structure dialog box appears on the screen.
06:39 Click and rotate the rotating tool that is present in the dialog box.
06:46 Observe the panel. The selected bond is now rotating.
06:51 Stop rotating when you reach the desired angle. Close the dialog box.
06:57 Clear the selection. We can also use Sequence option in the tools menu to highlight the chains.
07:05 Scroll down the tools menu and click on Sequence option.
07:10 Choose Sequence from the sub-menu.
07:13 A Show model sequence dialog box appears.
07:17 Click on chain A if you want to select chain A. Then click on show.
07:23 Another dialog box appears on screen with the amino acid sequence.
07:28 The amino acid residues are represented as single letter abbreviations.
07:34 Click on the sequence to select.
07:37 Observe the panel, Chain A is now highlighted.
07:41 Click on quit to close the window.
07:44 Go to Actions menu, scroll down to Color. Click on yellow option.
07:50 Chain A is now in yellow color. Clear the selection.
07:55 We can open more than one structure on the Chimera window.
07:59 To open a second structure: Scroll down the file menu.
08:03 Click on Fetch by ID.
08:06 A Fetch structure by ID dialog box opens.
08:11 Select PDB option. Then type the 4 letter PDB code.

For example to fetch human insulin, type 4ex1.

08:23 Click on fetch button.
08:25 The two protein structures are overlapped on the panel.
08:29 To separate the two overlapping structures: We have to selectively move one model on the panel.
08:36 Open the Command line using favorites menu.
08:39 The Command line appears at the bottom of the window.
08:43 Click to uncheck model zero, which represents leucine zipper.
08:48 Bring the cursor to the insulin structure: Hold the center mouse button.
08:54 Then Drag to move the insulin model to the desired location on the panel.

Release the mouse button.

09:01 To selectively remove model from the screen: Open the model panel using Favorites menu.
09:08 A Model Panel dialog box appears.
09:11 Select the model you want to remove, by clicking on the model ID.
09:16 For example I want to remove the insulin model from the screen.
09:21 Click on the model ID. Click on close option.
09:26 Observe the panel. The model of insulin is now removed from the screen.
09:32 Close the model panel window.
09:34 We have reached the end of this tutorial.
09:37 Let's summarize what we have learnt.
09:40 In this tutorial we have learnt to Show labels for atoms and residues.
09:46 Select atoms and residues using Select menu or by Picking.
09:51 Change the color and display of the residues.
09:55 Add, delete or change atoms , Rotate bonds
10:00 Open more than one model on the display window. Select and move the model.
10:06 For the assignment Open a structure of human insulin, pdb code 4ex1 on the Chimera window.
10:14 Color all the hydrophobic amino acid residues in blue.
10:19 Color all polar residues in red.
10:23 Your completed assignment should look as follows.
10:29 The video at the following link summarizes the Spoken Tutorial project.

Please download and watch it.

10:36 The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

10:45 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this Mission is available at the link shown

10:55 This is Snehalatha from IIT Bombay signing off. Thank you for joining.

Contributors and Content Editors

Jyotisolanki, PoojaMoolya, Sandhya.np14

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