UCSF-Chimera/C4/Attributes/English-timed
From Script | Spoken-Tutorial
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| 00:01 | Welcome to this tutorial on Attributes. |
| 00:05 | In this tutorial, we will learn to: change attributes of atoms, residues and models, |
| 00:13 | color atoms in a protein according to B-factor values, |
| 00:18 | color residues according to kdhydrophobicity values. |
| 00:24 | To follow this tutorial, you should be familiar with Chimera interface . If not, for relevant tutorials, please visit our website. |
| 00:33 | To record this tutorial, I am using Ubuntu OS version 14.04, Chimera version 1.10.2 , Mozilla Firefox browser 42.0 and a working internet connection. |
| 00:50 | Here, I have opened a Chimera window. |
| 00:54 | Using command line, open the structure of Leucine zipper. |
| 00:52 | On the command text box, type:, open 1zik. Press Enter. |
| 01:05 | The model on the panel is shown as ribbons. |
| 01:10 | Using Presets menu, change the display to Interactive 2 . |
| 01:14 | To hide water molecules, on the command line type: delete solvent. Press Enter. |
| 01:22 | To change the display to sticks, type: rep stick. Press Enter. |
| 01:30 | Add hydrogens to the structure, type: addh . |
| 01:36 | Now, let us learn how to change the attributes of atoms and residues for this structure. |
| 01:43 | Attributes are properties with names and values. |
| 01:47 | In Chimera, items such as atoms, bonds, residues and molecule models have Attributes. |
| 01:54 | There are different ways to change the Attributes. |
| 01:57 | Open the Model Panel using Favorites menu. |
| 02:01 | Model Panel dialog box appears on the screen. |
| 02:05 | Click on the attributes button on the right side of the panel. |
| 02:10 | Attributes dialog box for 1zik opens on the screen. |
| 02:15 | The dialog box has attribute list. |
| 02:18 | The list includes Molecule Attributes and its components- Atom, bond and residue attributes. |
| 02:28 | Select Molecule Attributes. |
| 02:31 | The available attributes are listed on the window. |
| 02:35 | For example - To change the display of aromatic rings, click on the button next to aromatic display. |
| 02:42 | Select True from the drop-down. |
| 02:45 | Select Aromatic ring style as disk. |
| 02:49 | Click on the color well next to aromatic color. |
| 02:53 | Select color from the color editor. |
| 02:56 | Close the dialog box. |
| 02:59 | Observe the panel. All the aromatic rings are shown with disks in the center. |
| 03:06 | Change the display of the structure to ball and stick. |
| 03:10 | On the command line, type: rep bs |
| 03:16 | On the attributes dialog box, change the Van der Walls radii of the atoms. |
| 03:22 | Change the value of ball scale to 0.5. Press Enter. |
| 03:27 | Observe the panel. The atoms are shown with larger atomic radii. |
| 03:33 | Again click on Molecular Attributes check box. |
| 03:38 | From the list, click on Component Atom Attributes. |
| 03:43 | In the corresponding window, click on atom style button . |
| 03:48 | The drop-down menu has many options. |
| 03:51 | Click on sphere to change the display to cpk. |
| 03:55 | Observe the panel. |
| 03:57 | Select dot to bring back the sticks display. |
| 04:02 | Now click on Component Bond Attributes. |
| 04:10 | Here, there are options to change bond style to stick or wire. |
| 04:13 | Click on Component Residue Attributes. |
| 04:17 | Here we have options to change the attributes of the ribbon. |
| 04:22 | Using Presets menu, change the display of the structure on the panel to ribbons. |
| 04:28 | Now clicking the Attribute dialog-box. |
| 04:32 | Now, in the Attribute dialog-box, click on the color well next to ribbon color. Select a ribbon color. |
| 04:41 | And click on close option to close the color editor. |
| 04:46 | There are options to change the cross-section of the ribbon and scaling. |
| 04:52 | Close the dialog box. |
| 04:55 | Again, change the display to atoms using Presets menu. |
| 05:00 | Attributes can also be changed using Tools menu. |
| 05:03 | Click on Tools menu, scroll down to Structure Analysis. |
| 05:09 | And select Render by Attribute option from the sub-menu. |
| 05:14 | Render by attribute dialog box opens. |
| 05:17 | Here we have options to change the attributes of atoms, residues, molecules, segmentation regions etc. |
| 05:27 | Select atoms. Click on Render. |
| 05:32 | Click on Attribute list to check for available options. |
| 05:37 | The list shows two options: bfactor and occupancy |
| 05:43 | These two attributes can be read from the input PDB file. |
| 05:48 | Choose bfactor. |
| 05:50 | A histogram of values will appear with colored vertical bars. |
| 05:55 | B-factor values are a measure of mobility in the macromolecule. |
| 06:01 | Atoms with low B-factor values belong to a part of the structure that is well ordered. |
| 06:08 | Atoms with large B-factor values belong to part of the structure that is very flexible. |
| 06:15 | PDB file for a protein structure contains B-factor information. |
| 06:21 | Back to the panel. |
| 06:23 | The vertical bars can be dragged along the histogram with the mouse. |
| 06:29 | The value of B-factor is displayed in the Value text box. |
| 06:34 | Drag the blue vertical bar to zero, red to 100. |
| 06:41 | Then fix the white bar at value 50. |
| 06:45 | Click on Colors button. |
| 06:48 | Check options for color atoms, keep opaque and color surfaces. |
| 06:55 | The default color palette is blue and red. |
| 06:59 | You can change the color palette, using drop-down menu. |
| 07:04 | Click on Apply button. |
| 07:07 | Observe the panel. Atoms with high B-factor values are shown in red and least in blue. |
| 07:16 | As expected, atoms with high B-factors are on the outside of the structure. |
| 07:22 | Now, let us change the attributes of Residues. |
| 07:26 | In the Select by Attribute dialog box, click on Attributes button. |
| 07:32 | From the drop-down, select residues. |
| 07:36 | Click on Render. |
| 07:38 | The attributes for residues include kdHydrophobicity scale. |
| 07:44 | Click on kdHydrophobicity from the drop-down menu. |
| 07:48 | The values are displayed in the histogram. |
| 07:52 | kdHydrophobicity scales are values that define relative hydrophobicity of amino acid residues. |
| 08:00 | KdHydrophobicity values are positive for hydrophobic residues and Negative values for polar residues. |
| 08:09 | Hydrophobicity of the residues can be shown with colors or worms. |
| 08:15 | Choose Colors. By default, some of the parameters are selected. |
| 08:21 | Click on Apply button. Observe the panel. |
| 08:26 | The hydrophobic residues are colored in red, and polar residues are colored in blue. |
| 08:33 | Click on Worms button. Click on Apply. |
| 08:38 | Observe the panel. |
| 08:41 | Worms are modified ribbons that vary in radius. |
| 08:47 | Most hydrophobic residues face the interior of the structure. |
| 08:52 | By default, the more hydrophobic residues will be shown with larger radius. |
| 09:00 | To return the structure to normal ribbon: |
| 09:03 | click on worm-style button and choose non-worm option. |
| 09:09 | Click on OK button. |
| 09:12 | Close the Chimera session using File menu. |
| 09:16 | Let's summarize, In this tutorial, we have learnt to: change attributes of atoms, residues and models, |
| 09:25 | color atoms in a protein according to B-factor values, |
| 09:30 | color residues according to kdHydrophobicity values. |
| 09:35 | As an assignment, Open a model of hemoglobin (PDB code: 2HCO) on the panel. Color the atoms according to B-factor values. |
| 09:44 | Color the residues according to kdHydrophobicity values. |
| 09:49 | This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
| 09:56 | We conduct workshops using Spoken Tutorials and give certificates. Please contact us. |
| 10:04 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 10:10 | This is Snehalatha from IIT Bombay, signing off.
Thank you for joining. |
