Sandhya.np14 at 10:43, 26 June 2018

2018-06-26T10:43:15Z

Sandhya.np14 at 10:41, 26 June 2018

2018-06-26T10:41:39Z

Sandhya.np14 at 10:40, 26 June 2018

2018-06-26T10:40:57Z

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Sandhya.np14 at 07:41, 26 June 2018

2018-06-26T07:41:05Z

PoojaMoolya: Created page with "{| border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on '''Surface Properties''' in '''Chimera'''. |- | 00:06 | In this tut..."

2017-11-06T10:29:12Z

Created page with "{| border=1 ! <center>Time</center> ! <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Surface Properties''' in '''Chimera'''. |- | 00:06 | In this tut..."

New page

{| border=1
! <center>Time</center>
! <center>Narration</center>

|-
| 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''' C'''oloring''' 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 lets 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''').<br/>

|-
| 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.

|}

@@ Line 75: / Line 75: @@
 |-
 | 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'''.

@@ Line 1: / Line 1: @@
 {| border=1
-! <center>Time</center>
+| <center>Time</center>
-! <center>Narration</center>
+| <center>Narration</center>
 |-

@@ Line 9: / Line 9: @@
 |-
 | 00:06
-| In this tutorial, we will learn to, Show surfaces for protein and '''DNA''' structures.
+| 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'''
+| create '''image'''s of protein surface colored by : '''Amino acid hydrophobicity''' and '''Electrostatic Potential'''.
 |-
 |00:22
-| To follow this tutorial you should be familiar with, '''Chimera interface'''.
+| 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
+| Here I am using:
+'''Ubuntu OS''' version '''14.04''',
-'''Ubuntu OS version.''' 14.04
+'''Chimera''' version '''1.10.2'''
-−
 '''Chimera version''' 1.10.2
 |-
 |00:42
-| '''Mozilla firefox browser''' 42.0. And a working Internet connection.
+| '''Mozilla firefox browser 42.0''' and a working internet connection.
 |-
@@ Line 39: / Line 36: @@
 |-
 | 00:52
-| Open a structure of '''RTX CPD''' toxin using command line.
+| Open a structure of '''RTX CPD toxin''' using '''command line'''.
 |-
@@ Line 47: / Line 44: @@
 |-
 |01:02
-| On the '''command line''' text box'''.'''
+| On the '''command line''' text box,
+Type: '''Open space 3eeb'''.
-Type, '''Open space 3eeb'''
 |-
 |01:10
 | '''3eeb '''is the''' pdb code '''for''' RTX CPD toxin.'''
+Press '''Enter'''.
-Press enter.
 |-
 | 01:18
-| The protein structure is displayed on the panel. It contains two copies of the protein.
+| 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 :
+| 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.
+| On the '''command line''' text box , type '''delete colon dot a.''' Press '''Enter'''.
 |-
@@ Line 75: / Line 70: @@
 |-
 | 01:48
-| Protease domain is bound to ligand '''inositol hexakisphosphate. '''
+| '''Protease''' domain is bound to ligand '''inositol hexakisphosphate. '''
 In short''' IHP '''and '''Sodium ion.'''

UCSF-Chimera/C2/Surface-Properties/English-timed - Revision history

Sandhya.np14 at 10:43, 26 June 2018

Sandhya.np14 at 10:41, 26 June 2018

Sandhya.np14 at 10:40, 26 June 2018

Sandhya.np14 at 07:41, 26 June 2018

PoojaMoolya: Created page with "{| border=1 ! Time ! Narration |- | 00:01 | Welcome to this tutorial on '''Surface Properties''' in '''Chimera'''. |- | 00:06 | In this tut..."