UCSF-Chimera/C2/Picking-and-Selection/English-timed - Revision history

Sandhya.np14 at 16:07, 25 June 2018

2018-06-25T16:07:51Z

Sandhya.np14 at 16:06, 25 June 2018

2018-06-25T16:06:10Z

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Sandhya.np14 at 14:45, 25 June 2018

2018-06-25T14:45:02Z

Jyotisolanki at 07:33, 22 November 2017

2017-11-22T07:33:12Z

Jyotisolanki at 06:56, 22 November 2017

2017-11-22T06:56:19Z

Jyotisolanki at 10:49, 21 November 2017

2017-11-21T10:49:29Z

Jyotisolanki at 08:19, 21 November 2017

2017-11-21T08:19:46Z

Jyotisolanki at 08:07, 21 November 2017

2017-11-21T08:07:41Z

PoojaMoolya: Created page with "{| border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on '''Picking and Selection '''using Chimera. |- | 00:06 | In this..."

2017-11-02T09:01:23Z

Created page with "{| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Picking and Selection '''using Chimera. |- | 00:06 | In this..."

New page

{| border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 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.

|}

@@ Line 37: / Line 37: @@
 |-
 |  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
-| '''Chimera''' version 1.10.2,
+| '''Chimera''' version '''1.10.2''',
 |-
 |  00:57
-| '''Mozilla firefox''' browser 35.0,
+| '''Mozilla firefox''' browser '''35.0''',
 |-
@@ Line 494: / Line 494: @@
 | 10:55
 |  This is Snehalatha from IIT Bombay,
- signing off. Thank you for joining.
+signing off. Thank you for joining.
 |}

@@ Line 5: / Line 5: @@
 |-
 |  00:01
-|  Welcome to this tutorial on '''Picking and Selection '''using Chimera.
+|  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'''.
+|  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'''.
+|  select atoms and '''residues''' using '''Select menu''' or by '''Picking''',
 |-
 |  00:17
-|  Change the color and display of the '''residues'''.
+|  change the color and display of the '''residues''',
 |-
 |  00:21
-|  Add, delete or change atoms ,  Rotate bonds
+|  add, delete or change atoms ,  rotate bonds,
 |-
 |  00:27
-|  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.
 |-
 | 00:34
-|  To follow this tutorial you should have knowledge of  Undergraduate '''Biochemistry'''.
+|  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.
+| 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
+|  To record this tutorial, I am using: '''Ubuntu Operating System''' version  14.04,
 |-
 |  00:52
-| '''Chimera''' version 1.10.2
+| '''Chimera''' version 1.10.2,
 |-
 |  00:57
-| '''Mozilla firefox''' browser 35.0
+| '''Mozilla firefox''' browser 35.0,
 |-
 |  01:01
-| And a working internet connection.
+| and a working internet connection.
 |-
@@ Line 65: / Line 65: @@
 |-
 |  01:20
-|  Individual components of the structure such as: residues, atoms, bonds etc can be modified using tools available in '''Chimera'''.
+|  Individual components of the structure such as: '''residue'''s, atoms, '''bond'''s etc. can be modified using tools available in '''Chimera'''.
 |-
@@ Line 73: / Line 73: @@
 |-
 |  01:34
-|  There are different ways to make a selection:  using the '''Select''' menu in the menu bar.
+|  There are different ways to make a selection:  using the '''Select''' menu in the menu bar,
 |-
 |  01:40
-|  '''Picking''' from the '''graphics''' window.
+|  '''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.
+|  typing '''command'''s on the '''command line''', Or by selecting '''Model Panel''' and '''Sequence''' option present in the '''Favorites''' menu.
 |-
 |  01:53
-|  Back to the Chimera window.
+|  Back to the '''Chimera window'''.
 |-
 | 01:55
-| '''Leucine zipper''' motif consists of periodic repetition of '''leucine''' residues.
+| '''Leucine zipper motif''' consists of periodic repetition of '''leucine''' residues.
 |-

@@ Line 378: / Line 378: @@
 |-
 | 08:23
-| Click on fetch button.
+| Click on '''fetch''' button.
 |-
@@ Line 436: / Line 436: @@
 |-
 | 09:32
-|Close the model panel window.
+|Close the '''model panel window'''.
 |-

@@ Line 344: / Line 344: @@
 |-
 |  07:41
-| Click on quit to close the window.
+| Click on '''quit''' to close the window.
 |-

@@ Line 139: / Line 139: @@
 |-
 |  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'''.
 |-

@@ Line 97: / Line 97: @@
 |-
 | 02:08
-|  From the presets menu choose '''interactive 2''' option'''.'''
+|  From the '''presets''' menu choose '''interactive 2''' option'''.'''
 |-

@@ Line 13: / Line 13: @@
 |-
 |  00:12
-|  Select atoms and '''residues''' using '''Select menu''' or by '''Picking'''.
+|  Select '''atoms''' and '''residues''' using '''Select menu''' or by '''Picking'''.
 |-