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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.
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10:04 The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India.
10:10 This is Snehalatha from IIT Bombay, signing off.

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Contributors and Content Editors

Jyotisolanki, Sandhya.np14