UCSF-Chimera/C2/Picking-and-Selection/English-timed
From Script | Spoken-Tutorial
| |
|
|---|---|
| 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. |
