UCSF-Chimera/C2/Surface-Properties/English-timed
From Script | Spoken-Tutorial
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| 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. |
