Difference between revisions of "UCSF-Chimera/C2/Picking-and-Selection/English-timed"
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| 00:01 | | 00:01 | ||
− | | Welcome to this tutorial on '''Picking and Selection '''using Chimera. | + | | Welcome to this tutorial on '''Picking and Selection '''using '''Chimera'''. |
|- | |- | ||
| 00:06 | | 00:06 | ||
− | | In this tutorial, we will learn to | + | | In this tutorial, we will learn to: show labels for atoms and '''residues''', |
|- | |- | ||
| 00:12 | | 00:12 | ||
− | | | + | | select atoms and '''residues''' using '''Select menu''' or by '''Picking''', |
|- | |- | ||
| 00:17 | | 00:17 | ||
− | | | + | | change the color and display of the '''residues''', |
|- | |- | ||
| 00:21 | | 00:21 | ||
− | | | + | | add, delete or change atoms , rotate bonds, |
|- | |- | ||
| 00:27 | | 00:27 | ||
− | | | + | | open more than one model on the display window, select and move the model. |
|- | |- | ||
| 00:34 | | 00:34 | ||
− | | To follow this tutorial you should have knowledge of | + | | To follow this tutorial, you should have knowledge of undergraduate Biochemistry. |
|- | |- | ||
| 00:40 | | 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 | | 00:47 | ||
− | | To record this tutorial, I am using | + | | 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''', |
|- | |- | ||
| 01:01 | | 01:01 | ||
− | | | + | | and a working internet connection. |
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| 01:20 | | 01:20 | ||
− | | Individual components of the structure such as: | + | | 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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| 01:34 | | 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 | | 01:40 | ||
− | | '''Picking''' from the '''graphics''' window | + | | '''Picking''' from the '''graphics''' window, |
|- | |- | ||
| 01:43 | | 01:43 | ||
− | | | + | | typing '''command'''s on the '''command line''', Or by selecting '''Model Panel''' and '''Sequence''' option present in the '''Favorites''' menu. |
|- | |- | ||
| 01:53 | | 01:53 | ||
− | | Back to the Chimera window. | + | | Back to the '''Chimera window'''. |
|- | |- | ||
| 01:55 | | 01:55 | ||
− | | '''Leucine zipper''' | + | | '''Leucine zipper motif''' consists of periodic repetition of '''leucine''' residues. |
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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 | + | | 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'''. | ||
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| 02:42 | | 02:42 | ||
− | | All the '''leucine''' | + | | All the '''leucine residue'''s are now highlighted. |
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| 03:03 | | 03:03 | ||
− | | '''Leucine''' being '''hydrophobic''' is packed into the '''hydrophobic''' | + | | '''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 | + | | To pick a '''residue''' from the '''screen''', hover the cursor over the structure. |
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| 03:26 | | 03:26 | ||
− | | It has information such as '''residue''' name, '''residue''' number and | + | | 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''' | + | | 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 | + | | 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 | + | | '''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 | + | | 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 | ||
− | | 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 | ||
− | | | + | | 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: | + | | 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. | + | |
|- | |- | ||
| 08:23 | | 08:23 | ||
− | | Click on fetch button. | + | | Click on '''fetch''' button. |
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| 08:29 | | 08:29 | ||
− | | To separate the two overlapping structures | + | | 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 | + | | Bring the cursor to the '''insulin''' structure, hold the center mouse button. |
|- | |- | ||
| 08:54 | | 08:54 | ||
− | | Then | + | | 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: | + | | 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 | + | | 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''', |
|- | |- | ||
| 09:51 | | 09:51 | ||
− | | | + | | change the color and display of the '''residues''', |
|- | |- | ||
| 09:55 | | 09:55 | ||
− | | | + | | 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. |
|- | |- | ||
| 10:06 | | 10:06 | ||
− | | For the assignment | + | | 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 | + | | 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 | + | |
|- | |- | ||
| 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
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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. |