Difference between revisions of "UCSF-Chimera/C2/Surface-Properties/English-timed"

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Line 62: Line 62:
 
|-
 
|-
 
| 01:33
 
| 01:33
−
| On the '''command line''' text box , type '''delete colon dot a.''' Press '''Enter'''.  
+
| On the '''command line''' text box , type: '''delete colon dot a.''' Press '''Enter'''.  
  
 
|-
 
|-
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|-
 
|-
 
| 01:48
 
| 01:48
−
| '''Protease''' domain is bound to ligand '''inositol hexakisphosphate. '''
+
| '''Protease domain''' is bound to '''ligand''' '''inositol hexakisphosphate. '''
−
 
+
In short,''' IHP '''and '''Sodium ion.'''
−
In short''' IHP '''and '''Sodium ion.'''
+
  
 
|-
 
|-
 
| 01:58
 
| 01:58
−
| Next delete the solvent molecules, present as red dots near the ligand.  
+
Next, delete the solvent molecules, present as red dots near the '''ligand'''.  
−
 
+
Type: '''delete space solvent'''. Press '''Enter'''.
−
Type '''delete space solvent'''. Press enter
+
  
 
|-
 
|-
 
| 02:09
 
| 02:09
−
| To delete the sodium ion which is present along with the ligand,
+
| To delete the '''sodium ion''' which is present along with the '''ligand''',
−
 
+
Type:'''delete ions'''. Press '''Enter'''.
−
Type,'''delete ions'''. Press enter.
+
  
 
|-
 
|-
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|-
 
|-
 
|02:29
 
|02:29
−
| Select '''Interactive 3''', hydrophobicity surface.
+
| Select '''Interactive 3''', '''hydrophobicity surface'''.
  
 
|-
 
|-
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|-
 
|-
 
|02:41
 
|02:41
−
| Blue for the most '''polar residues'''.
+
| Blue for the most '''polar residues''',
  
 
|-
 
|-
 
|02:45
 
|02:45
−
| Orange red for the most '''hydrophobic.''' And white for '''neutral residues'''.
+
| Orange red for the most '''hydrophobic''' and white for neutral '''residues'''.
  
 
|-
 
|-
 
|02:52
 
|02:52
−
| Proteins generally interact with other proteins and molecules via their surface regions
+
| Proteins generally interact with other proteins and molecules via their surface regions.
  
 
|-
 
|-
 
| 02:59
 
| 02:59
−
| Representing a protein by its molecular surface helps in: The study of protein folding.
+
| Representing a protein by its molecular surface helps in: the study of protein folding,
  
 
|-
 
|-
 
| 03:06
 
| 03:06
−
| Prediction of''' biomolecular recognition''',  
+
| prediction of biomolecular recognition,  
  
 
|-
 
|-
 
|03:09
 
|03:09
−
| Detection of '''drug binding cavities''' and '''Molecular Graphics'''.  
+
| detection of '''drug binding cavities''' and '''Molecular Graphics'''.  
  
 
|-
 
|-
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|-
 
|-
 
|03:18
 
|03:18
−
| Next to display '''electrostatic potential surface''' for the protein:
+
| Next, to display '''electrostatic potential surface''' for the protein,
  
 
|-
 
|-
 
| 03:24
 
| 03:24
−
| Click on the tools menu, scroll down to '''Surface\Binding Analysis. '''
+
| click on the '''Tools''' menu, scroll down to '''Surface\Binding Analysis. '''
  
 
|-
 
|-
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|-
 
|-
 
| 03:36
 
| 03:36
−
| A '''Coulombic Surface''' C'''oloring''' dialog box opens.
+
| A '''Coulombic Surface Coloring''' dialog box opens.
  
 
|-
 
|-
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|-
 
|-
 
| 03:45
 
| 03:45
−
| Default settings work well most of the time. Click on  '''OK''' button.
+
| '''Default''' settings work well most of the time. Click on  '''OK''' button.
  
 
|-
 
|-
 
| 03:51
 
| 03:51
−
| On the panel we have the protein showing '''electrostatic potential surface.'''
+
| On the panel, we have the protein showing '''electrostatic potential surface.'''
  
 
|-
 
|-
 
|03:57
 
|03:57
−
| Red color for negative '''potential'''. Blue for positive '''potential'''. And white for neutral.
+
| Red color for negative '''potential''', blue for positive '''potential''' and white for neutral.
  
 
|-
 
|-
 
| 04:07
 
| 04:07
−
| Now lets see how to create high quality images for publication, presentations etc:
+
| Now, let's see how to create high quality images for publication, presentations etc:
  
 
|-
 
|-
 
|04:14
 
|04:14
−
| Make the sticks of the '''inositol''' ligand a little thicker using the command Set attribute:
+
| Make the sticks of the '''inositol''' '''ligand''' a little thicker using the command '''Set attribute''':
−
 
+
'''setattr space m space stickScale 2'''. Press '''Enter'''.
−
'''setattr space m space stickScale 2'''. '''Press enter'''
+
  
 
|-
 
|-
 
| 04:35
 
| 04:35
−
| Use publication preset for nice image settings
+
| Use '''publication preset''' for nice image settings.
  
 
|-
 
|-
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|-
 
|-
 
| 04:54
 
| 04:54
−
| At this point we can adjust other parameters such as thickness of the line, lighting etc.
+
| At this point, we can adjust other parameters such as thickness of the line, lighting etc.
  
 
|-
 
|-
 
| 05:02
 
| 05:02
−
| Click on '''Tools menu''', scroll down and click on '''Viewing Controls.'''
+
| Click on '''Tools''' menu, scroll down and click on '''Viewing Controls.'''
  
 
|-
 
|-
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|-
 
|-
 
| 05:11
 
| 05:11
−
| A '''Viewing''' window opens with tabs to change different viewing settings:
+
| A '''Viewing''' window opens with '''tab'''s to change different viewing settings:
  
 
|-
 
|-
 
| 05:16
 
| 05:16
−
| Such as '''Camera, Sideview, Rotation, Effects, Lighting'''.
+
| such as '''Camera, Sideview, Rotation, Effects, Lighting'''.
  
 
|-
 
|-
 
| 05:23
 
| 05:23
−
| Under the '''lightings''' option: To view a simple '''line drawing '''appearance,  Click on the '''mode''' button, select '''ambient''' from the list.
+
| Under the '''lightings''' option, to view a simple line drawing appearance,  click on the '''mode''' button, select '''ambient''' from the list.
  
 
|-
 
|-
 
| 05:34
 
| 05:34
−
| Observe the panel.  
+
| Observe the '''panel'''.  
  
 
|-
 
|-
 
| 05:36
 
| 05:36
−
| To restore the default lighting mode: Select '''Two-point '''option.
+
| To restore the default lighting mode, select '''Two-point '''option.
  
 
|-
 
|-
 
| 05:42
 
| 05:42
−
| Click on''' close '''button to close the window'''.'''
+
| Click on''' close '''button to close the window.
  
 
|-
 
|-
 
| 05:46
 
| 05:46
−
| Save the image using '''Save image''' option in the '''File '''menu.
+
| '''Save''' the '''image''' using '''Save image''' option in the '''File '''menu.
  
 
|-
 
|-
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|-
 
|-
 
| 05:56
 
| 05:56
−
| Close the current session. Click on '''File menu'''  Scroll down and click on '''Close Session '''option'''.'''
+
| Close the current session. Click on '''File''' menu. Scroll down and click on '''Close Session '''option.
  
 
|-
 
|-
 
| 06:04
 
| 06:04
−
| Open the graphics window.  Fetch the structure of the '''DNA''' using '''command line'''.
+
| Open the '''graphics window'''.  Fetch the structure of the '''DNA''' using '''command line'''.
  
 
|-
 
|-
 
| 06:11
 
| 06:11
−
| On the command line text box.  Type, '''open 1d86 ''' Press enter.
+
| On the command line text box, type: '''open 1d86 ''', press '''Enter'''.
  
 
|-
 
|-
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|-
 
|-
 
| 06:39
 
| 06:39
−
| The '''nucleic acid sugars''' and '''bases''' are shown as '''tube and slab representations.'''
+
| The '''nucleic acid sugars''' and '''bases''' are shown as '''tube''' and '''slab''' representations.
  
 
|-
 
|-
 
| 06:46
 
| 06:46
−
| Scroll down the''' presets menu '''and click on '''interactive 2''' option.
+
| Scroll down the''' presets''' menu and click on '''interactive 2''' option.
  
 
|-
 
|-
 
| 06:53
 
| 06:53
−
| This will show the '''DNA''' as wire and '''netropsin''' as '''spheres.'''
+
| This will show the '''DNA''' as wire and '''netropsin''' as spheres.
  
 
|-
 
|-
 
| 06:59
 
| 06:59
−
| Type command to remove solvent. '''delete space solvent''' . Press enter'''.'''
+
| Type command to remove solvent: '''delete space solvent''' . Press '''Enter'''.'
  
 
|-
 
|-
 
| 07:09
 
| 07:09
−
| To show the surface for this structure, Scroll down the '''Actions menu''', select '''surface'''.
+
| To show the surface for this structure, scroll down the '''Actions''' menu, select '''surface'''.
−
 
+
 
From the sub-menu, select '''show'''.  
 
From the sub-menu, select '''show'''.  
  
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|-
 
|-
 
| 07:27
 
| 07:27
−
| '''Major groove''' and '''minor groove''' are clearly seen in this picture.
+
| Major groove and minor groove are clearly seen in this picture.
  
 
|-
 
|-
 
| 07:33
 
| 07:33
−
| The '''ligand, netropsin''' is seen bound in the '''minor groove'''.
+
| The '''ligand, netropsin''' is seen bound in the minor groove.
  
 
|-
 
|-
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|-
 
|-
 
| 07:41
 
| 07:41
−
| Scroll down the '''Action menu''', select '''Surface''' . Sub-menu has 3 options :  '''Solid, mesh and dot.'''
+
| Scroll down the '''Action''' menu, select '''Surface''' . Sub-menu has 3 options :  '''Solid, mesh and dot.'''
  
 
|-
 
|-
 
| 07:52
 
| 07:52
−
| By default surface is shown as solid.
+
| By default, surface is shown as solid.
  
 
|-
 
|-
 
| 07:57
 
| 07:57
−
| Click on '''mesh'''. To display mesh surface.
+
| Click on '''mesh''' to display mesh surface.
  
 
|-
 
|-
 
| 08:02
 
| 08:02
−
| Click on '''dot'''. To display the dot surface.
+
| Click on '''dot''' to display the dot surface.
  
 
|-
 
|-
 
| 08:07
 
| 08:07
−
| Click on '''solid''', to get back to solid surface.
+
| Click on '''solid''' to get back to solid surface.
  
 
|-
 
|-
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|-
 
|-
 
| 08:25
 
| 08:25
−
| For demonstration I will choose 50%.
+
| For demonstration, I will choose 50%.
  
 
|-
 
|-
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|-
 
|-
 
| 08:31
 
| 08:31
−
| To give a different color to the surface: Click on ''' Color '''option in the '''Actions''' menu, scroll down and click on '''all options'''.
+
| To give a different color to the surface: click on ''' Color '''option in the '''Actions''' menu, scroll down and click on '''all options'''.
  
 
|-
 
|-
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|-
 
|-
 
| 08:51
 
| 08:51
−
| Click on the radio button next to '''surfaces'''.
+
| Click on the '''radio button''' next to '''surfaces'''.
  
 
|-
 
|-
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|-
 
|-
 
| 09:02
 
| 09:02
−
| Observe the panel. The color of the surface is now changed to '''dim gray.'''
+
| Observe the panel. The color of the surface is now changed to dim gray.
−
 
+
 
Close the dialog box.
 
Close the dialog box.
  
 
|-
 
|-
 
| 09:11
 
| 09:11
−
| Save image using '''Save Image''' option in the '''File '''menu.
+
| '''Save''' image using '''Save Image''' option in the '''File '''menu.
  
 
|-
 
|-
 
| 09:16
 
| 09:16
−
| Let's summarize. In this tutorial we have learnt to Show '''Amino acid hydrophobicity ''' surface and '''Electrostatic Potential '''surface for protein and DNA structures.
+
| Let's summarize. In this tutorial, we have learnt to show '''Amino acid hydrophobicity ''' surface and '''Electrostatic Potential '''surface for protein and DNA structures.
  
 
|-
 
|-
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|-
 
|-
 
| 09:37
 
| 09:37
−
| Now for the assignment: Show''' amino acid hydrophobicity surface''' and '''electrostatic potential surface''' for the structure of '''human hemoglobin''' ('''pdb code: 2dn1''').<br/>  
+
| Now, for the assignment: Show''' amino acid hydrophobicity surface''' and '''electrostatic potential surface''' for the structure of '''human hemoglobin''' ('''pdb code: 2dn1''').<br/>  
  
 
|-
 
|-
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|-
 
|-
 
| 10:11
 
| 10:11
−
| The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.  
+
| The video at the following '''link''' summarizes the Spoken Tutorial project. Please download and watch it.  
  
 
|-
 
|-
 
| 10:18
 
| 10:18
−
| The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test.  
+
| 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.  
  
 
|-
 
|-
 
| 10:28
 
| 10:28
−
| 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 Mission is available at the link shown
+
  
 
|-
 
|-
 
| 10:39
 
| 10:39
−
| This is Snehalatha from IIT Bombay signing off. Thank you for joining.  
+
| This is Snehalatha from IIT Bombay, signing off. Thank you for joining.  
  
 
|}
 
|}

Revision as of 16:10, 26 June 2018

Time
Narration
00:01 Welcome to this tutorial on Surface Properties in Chimera.
00:06 In this tutorial, we will learn to: show surfaces for protein and DNA structures,
00:12 create images of protein surface colored by : Amino acid hydrophobicity and Electrostatic Potential.
00:22 To follow this tutorial, you should be familiar with Chimera interface.

If not, for relevant tutorials, please visit our website.

00:33 Here I am using:

Ubuntu OS version 14.04, Chimera version 1.10.2

00:42 Mozilla firefox browser 42.0 and a working internet connection.
00:49 Here I have opened the Chimera window.
00:52 Open a structure of RTX CPD toxin using command line.
00:58 Open the command line using Favorites menu.
01:02 On the command line text box,

Type: Open space 3eeb.

01:10 3eeb is the pdb code for RTX CPD toxin.

Press Enter.

01:18 The protein structure is displayed on the panel. It contains two copies of the protein.
01:26 Type commands on the command line to delete one of the copies, that is chain A.
01:33 On the command line text box , type: delete colon dot a. Press Enter.
01:43 Observe the panel, one of the copies of the enzyme is deleted.
01:48 Protease domain is bound to ligand inositol hexakisphosphate.

In short, IHP and Sodium ion.

01:58 
Next, delete the solvent molecules, present as red dots near the ligand.

Type: delete space solvent. Press Enter.

02:09 To delete the sodium ion which is present along with the ligand,

Type:delete ions. Press Enter.

02:19 Now we can display the structure of the protein using Presets option.
02:25 Click on Presets option in the menu bar.
02:29 Select Interactive 3, hydrophobicity surface.
02:34 This will display a molecular surface color-coded by amino acid hydrophobicity.
02:41 Blue for the most polar residues,
02:45 Orange red for the most hydrophobic and white for neutral residues.
02:52 Proteins generally interact with other proteins and molecules via their surface regions.
02:59 Representing a protein by its molecular surface helps in: the study of protein folding,
03:06 prediction of biomolecular recognition,
03:09 detection of drug binding cavities and Molecular Graphics.
03:15 Back to the Chimera window.
03:18 Next, to display electrostatic potential surface for the protein,
03:24 click on the Tools menu, scroll down to Surface\Binding Analysis.
03:30 From the sub-menu, choose coulombic surface coloring.
03:36 A Coulombic Surface Coloring dialog box opens.
03:41 The colors and associated values can be changed.
03:45 Default settings work well most of the time. Click on OK button.
03:51 On the panel, we have the protein showing electrostatic potential surface.
03:57 Red color for negative potential, blue for positive potential and white for neutral.
04:07 Now, let's see how to create high quality images for publication, presentations etc:
04:14 Make the sticks of the inositol ligand a little thicker using the command Set attribute:

setattr space m space stickScale 2. Press Enter.

04:35 Use publication preset for nice image settings.
04:40 Again scroll down the Presets menu, select Publication 1.
04:45 This will create an image with a white background, black outlines and increased smoothness of the edges.
04:54 At this point, we can adjust other parameters such as thickness of the line, lighting etc.
05:02 Click on Tools menu, scroll down and click on Viewing Controls.
05:08 Click on lighting from the sub-menu.
05:11 A Viewing window opens with tabs to change different viewing settings:
05:16 such as Camera, Sideview, Rotation, Effects, Lighting.
05:23 Under the lightings option, to view a simple line drawing appearance, click on the mode button, select ambient from the list.
05:34 Observe the panel.
05:36 To restore the default lighting mode, select Two-point option.
05:42 Click on close button to close the window.
05:46 Save the image using Save image option in the File menu.
05:51 Let us now look at the surface representation for a DNA structure.
05:56 Close the current session. Click on File menu. Scroll down and click on Close Session option.
06:04 Open the graphics window. Fetch the structure of the DNA using command line.
06:11 On the command line text box, type: open 1d86 , press Enter.
06:20 The structure is of a double helical DNA with a molecule of netropsin bound to it.
06:27 Netropsin is a polyamide with antibiotic and antiviral properties.
06:34 Initially this structure is shown as ribbons.
06:39 The nucleic acid sugars and bases are shown as tube and slab representations.
06:46 Scroll down the presets menu and click on interactive 2 option.
06:53 This will show the DNA as wire and netropsin as spheres.
06:59 Type command to remove solvent: delete space solvent . Press Enter.'
07:09 To show the surface for this structure, scroll down the Actions menu, select surface.

From the sub-menu, select show.

07:20 Observe the panel. The DNA structure is now displayed with the surface.
07:27 Major groove and minor groove are clearly seen in this picture.
07:33 The ligand, netropsin is seen bound in the minor groove.
07:38 There are 3 different ways to display surfaces.
07:41 Scroll down the Action menu, select Surface . Sub-menu has 3 options : Solid, mesh and dot.
07:52 By default, surface is shown as solid.
07:57 Click on mesh to display mesh surface.
08:02 Click on dot to display the dot surface.
08:07 Click on solid to get back to solid surface.
08:11 We can adjust the degree of transparency for the solid surface.
08:16 Go on Actions menu again, click on Surface.
08:20 Select Transparency option and choose the percentage option.
08:25 For demonstration, I will choose 50%.
08:29 Observe the panel.
08:31 To give a different color to the surface: click on Color option in the Actions menu, scroll down and click on all options.
08:41 A color Actions dialog box opens.
08:45 Change the “coloring applies to” setting to surfaces.
08:51 Click on the radio button next to surfaces.
08:55 Click on any color you like from the color panel. I will choose dim gray.
09:02 Observe the panel. The color of the surface is now changed to dim gray.

Close the dialog box.

09:11 Save image using Save Image option in the File menu.
09:16 Let's summarize. In this tutorial, we have learnt to show Amino acid hydrophobicity surface and Electrostatic Potential surface for protein and DNA structures.
09:30 Create high quality images for publication using different viewing settings.
09:37 Now, for the assignment: Show amino acid hydrophobicity surface and electrostatic potential surface for the structure of human hemoglobin (pdb code: 2dn1).
09:51 Color the hem ligand green. Your completed assignment should look as follows.
10:11 The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
10:18 The Spoken Tutorial project team conducts workshops and gives certificates for those who pass an online test.

For more details, please write to us.

10:28 Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India.

More information on this mission is available at the link shown.

10:39 This is Snehalatha from IIT Bombay, signing off. Thank you for joining.

Contributors and Content Editors

PoojaMoolya, Sandhya.np14

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