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

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

Contributors and Content Editors

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