Difference between revisions of "UCSF-Chimera/C4/Attributes/English-timed"

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(Created page with "{| border=1 | <center>Time</center> | <center>Narration</center> |- |00:01 | Welcome to this tutorial on '''Attributes.''' |- |00:05 | In this tutorial we will learn to, Ch...")
 
 
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|00:05
 
|00:05
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| In this tutorial we will learn to, Change '''attributes''' of atoms, residues and models.
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| In this tutorial, we will learn to: change '''attributes''' of atoms, residues and models,
  
 
|-
 
|-
 
|00:13
 
|00:13
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| Color atoms in a protein according to '''B-factor''' values.
+
| color atoms in a protein according to '''B-factor''' values,
 
   
 
   
 
|-
 
|-
 
|00:18
 
|00:18
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|Color residues according to '''kdhydrophobicity''' values.
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|color residues according to '''kdhydrophobicity''' values.
  
 
|-
 
|-
 
|00:24
 
|00:24
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| To follow this tutorial you should be familiar with '''Chimera''' interface . If not, for relevant tutorials, please visit our website.  
+
| To follow this tutorial, you should be familiar with '''Chimera''' interface . If not, for relevant tutorials, please visit our '''website'''.  
  
 
|-
 
|-
 
|00:33  
 
|00:33  
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| 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.
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| 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
 
|00:50
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| Here I have opened a '''Chimera''' window.
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| Here, I have opened a '''Chimera''' window.
  
 
|-
 
|-
 
|00:54
 
|00:54
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|Using command line open the structure of '''Leucine zipper. '''
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|Using '''command line''', open the structure of '''Leucine zipper. '''
  
 
|-
 
|-
 
| 00:52
 
| 00:52
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|On the command text box, type, '''open 1zik'''  Press '''Enter'''.
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|On the '''command''' text box, type:, '''open 1zik'''. Press '''Enter'''.
  
 
|-
 
|-
 
|01:05  
 
|01:05  
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| The model on the panel is shown as '''ribbons'''.
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| The model on the '''panel''' is shown as '''ribbons'''.
  
 
|-
 
|-
 
|01:10  
 
|01:10  
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|Using '''Presets''' menu, change the display to '''Interactive 2''' '''. '''
+
|Using '''Presets''' menu, change the display to '''Interactive 2''' .  
  
 
|-
 
|-
 
|01:14
 
|01:14
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| To hide water molecules, on the '''command line''' type, '''delete solvent'''. Press '''Enter'''.
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| To hide water molecules, on the '''command line''' type: '''delete solvent'''. Press '''Enter'''.
  
 
|-
 
|-
 
|01:22   
 
|01:22   
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| To change the display to sticks, type, '''rep stick''' , Press '''Enter'''.
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| To change the display to '''sticks''', type: '''rep stick'''. Press '''Enter'''.
  
 
|-
 
|-
 
|01:30
 
|01:30
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| Add hydrogens to the structure, type, '''addh '''
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| Add hydrogens to the structure, type: '''addh '''.
  
 
|-
 
|-
 
|01:36  
 
|01:36  
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| Now let us learn how to change the '''attributes '''of '''atoms and residues''' for this structure.
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| Now, let us learn how to change the '''attributes '''of atoms and '''residues''' for this structure.
  
 
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|-
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|-
 
|-
 
|01:47   
 
|01:47   
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|In '''Chimera''', items such as '''atoms, bonds, residues''' and '''molecule models''' have '''Attributes.'''
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|In '''Chimera''', items such as '''atoms, bonds, residues''' and molecule models have '''Attributes.'''
  
 
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|-
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|-
 
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|02:01  
 
|02:01  
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| '''Model Panel''' dialog box appears on the screen.
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| '''Model Panel''' dialog box appears on the '''screen'''.
  
 
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|-
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|-
 
|-
 
|02:18   
 
|02:18   
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| The list includes. '''Molecule Attributes''' and its components, '''Atom, bond '''and''' residue attributes.'''
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| The list includes '''Molecule Attributes''' and its components- '''Atom, bond '''and''' residue attributes.'''
  
 
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|02:59   
 
|02:59   
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| Observe the panel. All the '''aromatic rings''' are shown with disks in the center.
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| Observe the panel. All the '''aromatic rings''' are shown with '''disk'''s in the center.
  
 
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|-
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|-
 
|-
 
|03:10
 
|03:10
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|On the command line, type, '''rep bs'''
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|On the '''command line''', type: '''rep bs'''
  
 
|-
 
|-
 
|03:16  
 
|03:16  
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| On the attributes dialog box, change the Van der Walls radii of the atoms.
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| On the '''attributes''' dialog box, change the '''Van der Walls''' radii of the atoms.
  
 
|-
 
|-
 
|03:22  
 
|03:22  
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|Change the value of '''ball scale''' to 0.5. Press '''Enter'''.
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|Change the value of '''ball scale''' to '''0.5'''. Press '''Enter'''.
  
 
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|-
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|03:43   
 
|03:43   
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| In the corresponding window, click on '''atom style button''' .
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| In the corresponding window, click on '''atom style''' button .
  
 
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|04:17
 
|04:17
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|Here we have options to change the attributes of the ribbon.
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|Here we have options to change the attributes of the '''ribbon'''.
  
 
|-
 
|-
 
|04:22  
 
|04:22  
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| Using '''presets''' menu, change the display of the structure on the panel to '''ribbons'''.
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| Using '''Presets''' menu, change the display of the structure on the panel to '''ribbons'''.
 
|-
 
|-
 
|04:28   
 
|04:28   
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|Now Clicking the '''Attribute''' dialog-box.
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|Now clicking the '''Attribute''' dialog-box.
  
 
|-
 
|-
 
|04:32  
 
|04:32  
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| Now,in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''.  Select a ribbon color.
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| Now, in the '''Attribute''' dialog-box, click on the '''color well '''next to '''ribbon color'''.  Select a ribbon color.
  
 
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|05:50  
 
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|A '''histogram''' of values will appear, with colored vertical bars.
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|A '''histogram''' of values will appear with colored vertical bars.
  
 
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|06:01
 
|06:01
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| '''Atoms''' with low '''B-factor''' values belong to a part of the structure that is well ordered.  
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| Atoms with low '''B-factor''' values belong to a part of the structure that is well ordered.  
  
 
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|06:15  
 
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| PDB file for a '''protein''' structure contains B-factor information.  
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| '''PDB file''' for a '''protein''' structure contains B-factor information.  
  
 
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|06:23
 
|06:23
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|The vertical bars can be dragged along the '''histogram''' with the mouse.
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|The vertical bars can be dragged along the '''histogram''' with the '''mouse'''.
  
 
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|06:55
 
|06:55
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|The default color '''palette''' is blue and red.
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|The '''default''' color '''palette''' is blue and red.
  
 
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|07:07  
 
|07:07  
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| Observe the panel. '''Atoms''' with high '''B-factor''' values are shown in red and least in blue.
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| Observe the panel. Atoms with high '''B-factor''' values are shown in red and least in blue.
  
 
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|07:16  
 
|07:16  
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| As expected, '''atoms''' with high '''B-factors''' are on the outside of the structure.  
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| As expected, atoms with high '''B-factors''' are on the outside of the structure.  
  
 
|-
 
|-
 
|07:22  
 
|07:22  
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| Now let us change the '''attributes''' of '''Residues'''.
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| Now, let us change the '''attributes''' of '''Residues'''.
  
 
|-
 
|-
 
|07:26  
 
|07:26  
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| In the '''Select by Attribute''' dialog box, click on '''Attributes button.'''
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| In the '''Select by Attribute''' dialog box, click on '''Attributes''' button.
  
 
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|07:48  
 
|07:48  
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|The values are displayed in the histogram.
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|The values are displayed in the '''histogram'''.
  
 
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|08:41
 
|08:41
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|'''Worms''' are modified ribbons that vary in radius.  
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|'''Worms''' are modified '''ribbon'''s that vary in radius.  
  
 
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|09:03
 
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|Click on worm-style button and choose '''non-worm''' option.  
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|click on '''worm-style''' button and choose '''non-worm''' option.  
  
 
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|09:16  
 
|09:16  
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| Let's summarize, In this tutorial we have learnt to,  Change '''attributes''' of '''atoms, residues '''and''' models.'''
+
| Let's summarize, In this tutorial, we have learnt to: change '''attributes''' of '''atoms, residues '''and''' models,'''
  
 
|-
 
|-
 
|09:25  
 
|09:25  
−
|Color '''atoms''' in a '''protein''' according to '''B-factor''' values.
+
|color atoms in a '''protein''' according to '''B-factor''' values,
  
 
|-
 
|-
 
|09:30  
 
|09:30  
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| Color '''residues''' according to '''kdHydrophobicity '''values.
+
| color '''residues''' according to '''kdHydrophobicity '''values.
  
 
|-
 
|-
 
|09:35  
 
|09:35  
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| As an '''Assignment,'''  Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. Color the atoms according to '''B-factor''' values.
+
| As an '''assignment,'''  Open a model of '''hemoglobin (PDB code: 2HCO)''' on the panel. Color the atoms according to '''B-factor''' values.
 
   
 
   
 
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|09:49  
 
|09:49  
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| This video summarizes the Spoken Tutorial project If you do not have good bandwidth, you can download and watch it.
+
| This video summarizes the '''Spoken Tutorial''' project. If you do not have good bandwidth, you can download and watch it.
  
 
|-
 
|-
 
|09:56
 
|09:56
−
|  We conduct workshops using Spoken Tutorials and give certificates.Please contact us.
+
|  We conduct workshops using Spoken Tutorials and give certificates. Please contact us.
  
 
|-
 
|-
 
|10:04
 
|10:04
−
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.  
+
| The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.  
  
 
|-
 
|-
 
|10:10  
 
|10:10  
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| This is Snehalatha from IIT Bombay signing off.  
+
| This is Snehalatha from IIT Bombay, signing off.  
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 16:16, 28 June 2018

Time
Narration
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.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14

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