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

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|-
 
|-
 
|  00:47
 
|  00:47
−
|  To record this tutorial, I am using: '''Ubuntu Operating System''' version  14.04,
+
|  To record this tutorial, I am using: '''Ubuntu Operating System''' version  '''14.04''',
  
 
|-
 
|-
 
|  00:52
 
|  00:52
−
| '''Chimera''' version 1.10.2,
+
| '''Chimera''' version '''1.10.2''',
  
 
|-
 
|-
 
|  00:57
 
|  00:57
−
| '''Mozilla firefox''' browser 35.0,
+
| '''Mozilla firefox''' browser '''35.0''',
  
 
|-
 
|-
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|-
 
|-
 
| 02:08
 
| 02:08
−
|  From the '''presets''' menu choose '''interactive 2''' option'''.'''
+
|  From the '''presets''' menu, choose '''interactive 2''' option.
  
 
|-
 
|-
 
| 02:12
 
| 02:12
−
| This will convert the structure to atoms display. From the''' Select''' menu choose '''Residue''' option.  
+
| This will convert the structure to atoms display. From the''' Select''' menu, choose '''Residue''' option.  
  
 
|-
 
|-
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|-
 
|-
 
|  02:23
 
|  02:23
−
|  The Amino acid category menu has amino acids grouped as: '''aliphatic''', '''aromatic''', '''hydrophobic''', '''polar''' etc.
+
|  The '''Amino acid category''' menu has amino acids grouped as '''aliphatic, aromatic, hydrophobic, polar''' etc.
  
 
|-
 
|-
 
|  02:34
 
|  02:34
−
|  Standard amino acid menu has list of amino acid residues present in the structure.
+
|  '''Standard amino acid''' menu has list of amino acid residues present in the structure.
−
 
+
 
Click on '''leucine'''.
 
Click on '''leucine'''.
  
 
|-
 
|-
 
|  02:42
 
|  02:42
−
| All the '''leucine''' residues are now highlighted.  
+
| All the '''leucine residue'''s are now highlighted.  
  
 
|-
 
|-
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|-
 
|-
 
|  03:03
 
|  03:03
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|  '''Leucine''' being '''hydrophobic''' is packed into the '''hydrophobic''' core of the protein.
+
|  '''Leucine''' being '''hydrophobic''', is packed into the '''hydrophobic core''' of the protein.
  
 
|-
 
|-
 
|  03:09
 
|  03:09
−
|  Now change the display to ribbons using '''presets''' option. Click on '''Interactive 1'''.
+
|  Now, change the display to '''ribbons''' using '''presets''' option. Click on '''Interactive 1'''.
  
 
|-
 
|-
 
|  03:17
 
|  03:17
−
|  To pick a '''residue''' from the screen : Hover the cursor over the structure.
+
|  To pick a '''residue''' from the '''screen''', hover the cursor over the structure.
  
 
|-
 
|-
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|-
 
|-
 
| 03:26
 
| 03:26
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| It has information such as '''residue''' name, '''residue''' number and Chain.
+
| It has information such as '''residue''' name, '''residue''' number and '''chain'''.
  
 
|-
 
|-
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|-
 
|-
 
|  03:36
 
|  03:36
−
|  Bring the cursor to the first '''residue''' on chain A, that is '''arginine'''.
+
|  Bring the cursor to the first '''residue''' on '''chain A''', that is '''arginine'''.
  
 
|-
 
|-
 
|  03:41
 
|  03:41
−
|  Press and hold the CTRL key on the keyboard and click the left mouse button.
+
|  Press and hold the '''CTRL''' key on the keyboard and click the left '''mouse''' button.
−
Release the CTRL key.
+
Release the '''CTRL''' key.
  
 
|-
 
|-
 
|  03:49
 
|  03:49
−
|  The outline of the '''residue''' is highlighted. By default the selection is outlined in green.
+
|  The outline of the '''residue''' is highlighted. By default, the selection is outlined in green.
  
 
|-
 
|-
 
|  03:57
 
|  03:57
−
|  If you want to select more than one '''residue'''; Press and hold both CTRL and shift key on the key board.
+
|  If you want to select more than one '''residue''': press and hold both '''CTRL''' and '''shift''' key on the key board.
  
 
|-
 
|-
 
| 04:04
 
| 04:04
−
| Hover the mouse over the peptide chain.  Click on the '''residues''' you want to pick.  
+
| Hover the '''mouse''' over the '''peptide chain'''.  Click on the '''residues''' you want to pick.  
  
 
|-
 
|-
 
| 04:10
 
| 04:10
−
| Release the CTRL and Shift keys from the keyboard.  
+
| Release the '''CTRL''' and '''Shift''' keys from the keyboard.  
  
 
|-
 
|-
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|-
 
|-
 
| 04:23
 
| 04:23
−
| For example to display atoms, choose '''atoms/bonds.'''
+
| For example: to display atoms, choose '''atoms/bonds.'''
−
 
+
 
Click on '''Show'''.
 
Click on '''Show'''.
  
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|-
 
|-
 
|  04:42
 
|  04:42
−
|  Place the cursor over an object such as an atom, or bond.
+
|  Place the cursor over an object such as an atom or bond.
  
 
|-
 
|-
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|-
 
|-
 
|  04:52
 
|  04:52
−
|  '''Atomspec balloon''' for an atom has information such as: '''Residue''' name, number, chain and atom name.
+
|  '''Atomspec balloon''' for an atom has information such as '''Residue''' name, number, chain and atom name.
  
 
|-
 
|-
 
| 05:01
 
| 05:01
−
|  To select an atom, press and hold the CTRL key on the keyboard.
+
|  To select an atom, press and hold the '''CTRL''' key on the keyboard.
  
 
|-
 
|-
 
| 05:06
 
| 05:06
−
| While holding the CTRL key click on the atom you want to change.
+
| While holding the '''CTRL''' key, click on the atom you want to change.
  
 
|-
 
|-
 
|  05:11
 
|  05:11
−
|  The atom is now highlighted. To modify the atom double-click on the atom while holding the CTRL key.
+
|  The atom is now highlighted. To modify the atom, double-click on the atom while holding the '''CTRL''' key.
  
 
|-
 
|-
 
|  05:20
 
|  05:20
−
|  A '''''context menu '''''opens with options.  
+
|  A '''context menu '''opens with options.  
  
 
|-
 
|-
 
|  05:24
 
|  05:24
−
| Click on '''Modify-atom''' option. Release the CTRL key.
+
| Click on '''Modify-atom''' option. Release the '''CTRL''' key.
  
 
|-
 
|-
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|-
 
|-
 
|  05:33
 
|  05:33
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| Let us change the selected atom that is Nitrogen to a methyl group.
+
| Let us change the selected atom, that is Nitrogen, to a methyl group.
  
 
|-
 
|-
 
|  05:38
 
|  05:38
−
| The '''Build Structure''' window, Select element as carbon, bonds as 4  and Click on apply button.
+
| In the '''Build Structure''' window, select '''Element''' as '''carbon''', '''Bonds''' as 4  and click on '''Apply''' button.
  
 
|-
 
|-
 
|  05:49
 
|  05:49
−
|  Observe the panel.
+
|  Observe the '''panel'''.
  
 
|-
 
|-
 
| 05:51
 
| 05:51
 
| A methyl group is now added to the existing structure.  
 
| A methyl group is now added to the existing structure.  
−
 
 
Close the window.
 
Close the window.
  
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|-
 
|-
 
|  06:09
 
|  06:09
−
|  To select a bond, place the cursor on the bond.
+
|  To select a '''bond''', place the cursor on the bond.
  
 
|-
 
|-
 
| 06:13
 
| 06:13
−
| Press and hold the CTRL key.  Click the left mouse button.
+
| Press and hold the '''CTRL''' key.  Click the left '''mouse''' button.
  
 
|-
 
|-
 
|  06:18
 
|  06:18
−
|  The selected bond is now highlighted. While still holding the CTRL key double click on the bond.
+
|  The selected bond is now highlighted. While still holding the '''CTRL''' key, double click on the bond.
  
 
|-
 
|-
 
|  06:26
 
|  06:26
−
| Release the CTRL key on the key board.
+
| Release the '''CTRL''' key on the key board.
  
 
|-
 
|-
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|-
 
|-
 
|  07:34
 
|  07:34
−
| Click on the sequence to select.
+
| Click on the '''sequence''' to select.
  
 
|-
 
|-
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|-
 
|-
 
|  07:59
 
|  07:59
−
|  To open a second structure: Scroll down the file menu.
+
|  To open a second structure: scroll down the file menu.
  
 
|-
 
|-
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|  08:11
 
|  08:11
 
|  Select '''PDB''' option. Then type the 4 letter '''PDB code'''.
 
|  Select '''PDB''' option. Then type the 4 letter '''PDB code'''.
−
 
+
For example: to fetch '''human insulin''', type 4ex1.
−
For example to fetch '''human insulin''', type 4ex1.
+
  
 
|-
 
|-
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|-
 
|-
 
|  08:29
 
|  08:29
−
|  To separate the two overlapping structures: We have to selectively move one model on the panel.
+
|  To separate the two overlapping structures, we have to selectively move one model on the panel.
  
 
|-
 
|-
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|-
 
|-
 
|  08:48
 
|  08:48
−
|  Bring the cursor to the '''insulin''' structure: Hold the center mouse button.
+
|  Bring the cursor to the '''insulin''' structure, hold the center mouse button.
  
 
|-
 
|-
 
| 08:54
 
| 08:54
−
| Then Drag to move the '''insulin''' model to the desired location on the panel.
+
| Then drag to move the '''insulin''' model to the desired location on the panel.
−
 
+
 
Release the mouse button.
 
Release the mouse button.
  
 
|-
 
|-
 
|  09:01
 
|  09:01
−
|  To selectively remove model from the screen: Open the model panel using '''Favorites''' menu.
+
|  To selectively remove model from the screen: open the '''Model panel''' using '''Favorites''' menu.
  
 
|-
 
|-
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|-
 
|-
 
| 09:16
 
| 09:16
−
|For example I want to remove the '''insulin''' model from the screen.  
+
|For example, I want to remove the '''insulin''' model from the screen.  
  
 
|-
 
|-
 
| 09:21
 
| 09:21
−
|  Click on the '''model ID'''.  Click on close option.
+
|  Click on the '''model ID'''.  Click on '''close''' option.
  
 
|-
 
|-
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|-
 
|-
 
| 09:32
 
| 09:32
−
|Close the '''model panel window'''.
+
|Close the '''model panel''' window.
  
 
|-
 
|-
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|-
 
|-
 
| 09:40
 
| 09:40
−
|  In this tutorial we have learnt to  Show labels for atoms and '''residues'''.
+
|  In this tutorial, we have learnt to: show labels for atoms and '''residues''',
  
 
|-
 
|-
 
| 09:46
 
| 09:46
−
| Select atoms and residues using '''Select''' menu or by '''Picking'''.
+
| select atoms and residues using '''Select''' menu or by '''Picking''',
  
 
|-
 
|-
 
| 09:51
 
| 09:51
−
| Change the color and display of the '''residues'''.
+
| change the color and display of the '''residues''',
  
 
|-
 
|-
 
| 09:55
 
| 09:55
−
| Add, delete or change atoms ,  Rotate bonds
+
| add, delete or change atoms ,  rotate bonds,
  
 
|-
 
|-
 
|  10:00
 
|  10:00
−
|  Open more than one model on the display window. Select and move the model.
+
|  open more than one model on the display window, select and move the model.
  
 
|-
 
|-
 
| 10:06
 
| 10:06
−
|  For the assignment Open a structure of '''human insulin''', '''pdb code 4ex1''' on the Chimera window.
+
|  For the assignment: open a structure of '''human insulin''', '''pdb code 4ex1''' on the '''Chimera window'''.
  
 
|-
 
|-
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|-
 
|-
 
|  10:29
 
|  10:29
−
|  The video at the following link summarizes the Spoken Tutorial project.  
+
|  The video at the following '''link''' summarizes the '''Spoken Tutorial''' project. Please download and watch it.  
−
 
+
−
Please download and watch it.  
+
  
 
|-
 
|-
 
| 10:36
 
| 10:36
−
|  The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.  
+
|  The '''Spoken Tutorial''' project team conducts workshops and gives certificates for those who pass an online test.  
−
 
+
 
For more details, please write to us.  
 
For more details, please write to us.  
  
 
|-
 
|-
 
|  10:45
 
|  10:45
−
|  Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.  
+
|  Spoken Tutorial Project is funded by '''NMEICT, MHRD''', Government of India.  
−
 
+
More information on this mission is available at the link shown.
−
More information on this Mission is available at the link shown
+
  
 
|-
 
|-
 
| 10:55
 
| 10:55
−
|  This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
|  This is Snehalatha from IIT Bombay,
 +
signing off. Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 21:37, 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 In 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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