UCSF-Chimera/C2/Surface-Properties/English

Visual Cue	Narration
Slide Number 1 Title Slide	Welcome to this tutorial on Surface Properties in Chimera.
Slide Number 2 Learning Objectives	In this tutorial, we will learn to, Show surfaces for protein and DNA structures. Create images of protein surface colored by : Amino acid hydrophobicity And Electrostatic Potential
Slide Number 3 Pre-requisites	To follow this tutorial you should be familiar with, Chimera interface. If not, for relevant tutorials, please visit our website.
Slide Number 4 System Requirement	Here I am using Ubuntu OS version. 14.04 Chimera version 1.10.2 Mozilla firefox browser 42.0 And a working Internet connection.
Double-click on the chimera icon. Click on the lighting bolt icon to open graphics window.	Here I have opened the Chimera window.
Click on Fetch by ID option in the file menu. Type the pdb code 3eeb. Click on fetch button. (V. CHOLERAE RTX TOXIN)	Open a structure of RTX CPD toxin using command line. Open the command line using Favorites menu. On the command line text box. Type, Open space 3eeb 3eeb is the pdb code for RTX CPD toxin. Press enter.
Cursor on the panel. Zoom-in and rotate the structure.	The protein structure is displayed on the panel. It contains two copies of the protein.
Cursor on the panel.	Type commands on the command line to: Delete one of the copies, that is chain A :
Click on Favorites menu, click on command line. Type delete:.a press enter	On the command line text box , Type delete colon dot a. press enter.
Cursor on the panel.	Observe the panel, one of the copies of the enzyme is deleted.
Zoom-in and rotate the structure.	Protease domain is bound to ligand inositol hexakisphosphate. In short IHP and Sodium ion.
Type del solvent Press enter	Next delete the solvent molecules, present as red dots near the ligand. Type delete solvent Press enter
Type, del ions press enter.	To delete the sodium ion which is present along with the ligand, Type, delete ions press enter.
Click on Presets option, then click on Interactive 3, hydrophobicity surface.	Now we can display the structure of the protein using Presets option. Click on Presets option in the menu bar. Select Interactive 3, hydrophobicity surface.
Cursor on the panel.	This will display a molecular surface color-coded by amino acid hydrophobicity. Blue for the most polar residues. Orange red for the most hydrophobic. And white for neutral residues.
Slide Number 5 Protein surface	Proteins generally interact with other proteins and molecules via their surface regions
Slide Number 6 Protein Surface	Representing a protein by its molecular surface helps in: The study of protein folding. Prediction of biomolecular recognition, Detection of drug binding cavities. and Molecular Graphics.
Click on tools menu, surface\binding analysis. Choose coulumbic surface coloring from the sub-menu.	Back to the Chimera window. Next to display electrostatic potential surface for the protein: Click on the tools menu, scroll down to Surface\Binding Analysis. From the sub-menu, choose coulombic surface coloring.
Cursor on coulumbic surface coloring dialog box .	A Coulombic Surface Coloring dialog box opens. The colors and associated values can be changed. Default settings work well most of the time. Click OK button.
Cursor on the panel. Point to all the colored parts on the Panel.	On the panel we have the protein showing electrostatic potential surface. Red color for negative potential. Blue for positive potential. And white for neutral.
Zoom-in. Type: setattr m stickScale 2	Now lets see how to create high quality images for publication, presentations etc: Make the sticks of the inositol ligand a little thicker using the command Set attribute: setattr space m space stickScale 2 Press enter
Scroll down the presets menu and select Publication 1.	Use publication preset for nice image settings, Again scroll down the presets menu and select Publication 1. This will create an image with a white background, black outlines. And increased smoothness of the edges.
Cursor on the screen.	At this point we can adjust other parameters such as thickness of the line, lighting etc.
Click on Tools menu, scroll down and click on Viewing Controls. From the sub-menu select lighting.	Click on Tools menu, scroll down and click on Viewing Controls. Click on lighting from the sub-menu.
Cursor on the viewing window.	A Viewing window opens with tabs to change different viewing settings: Such as Camera, Sideview, Rotation, Effects, Lighting.
Click on the mode button and 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.
Cursor on the panel.	Observe the panel.
Select Two-point option from the list. Click on close button to close the window.	To restore the default lighting mode: Select Two-point option. Click on close button to close the window.
	Save the image using Save image option in the File menu.
Click on File menu, then click on Close Session. Click on Lighting bolt icon.	Let us now look at the surface representation for a DNA structure. Close the current session. Click on File menu. Scroll down and click on Close Session option. Open the graphics window. Fetch the structure of the DNA using command line.
Open Command line using Favorites menu. Type, open 1d86 Press enter point to netropsin.	On the command line text box. Type, open 1d86 Press enter. The structure is of a double helical DNA with a molecule of netropsin bound to it. Netropsin is a polyamide with antibiotic and antiviral properties.
Cursor on the structure.	Initially this structure is shown as ribbons. The nucleic acid sugars and bases are shown as tube and slab representations.
Scroll down the presets menu and click on interactive 2 option.	Scroll down the presets menu and click on interactive 2 option. This will show the DNA as wire and netropsin as spheres.
On the command line. Type, del solvent	Type command to remove solvent. delete solvent Press enter.
Scroll down the Actions menu, select surface. From sub-menu select show.	To show the surface for this structure, Scroll down the Actions menu, select surface. From the sub-menu, select show.
Cursor on the structure. Rotate the structure.	Observe the panel. The DNA structure is now displayed with the surface. Major groove and minor groove are clearly seen in this picture. The ligand, netropsin is seen bound in the minor groove.
Scroll down the Action menu, select Surface option. Cursor on sub-menu.	There are 3 different ways to display surfaces. Scroll down the Action menu, select Surface . Sub-menu has 3 options : Solid, mesh and dot. By default surface is shown as solid.
Click on mesh. Click on dot. Click on solid.	Click on mesh. To display mesh surface. Click on dot. To display the dot surface. Click on solid, to get back to solid surface.
Click on the transparency option. Select 20% option.	We can adjust the degree of transparency for the solid surface. Click on Actions menu again, click on Surface. Select Transparency option. Choose the percentage option. For demonstration I will choose 50%.
	Observe the panel.
Click on Color option in the Actions menu, scroll down and click on all options. A color Actions dialog box opens.	To give a different color to the surface: Click on Color option in the Actions menu, scroll down and click on all options. A color Actions dialog box opens.
Click on the radio button next to surfaces.	Change the “coloring applies to” setting to surfaces. Click on the radio button next to surfaces.
Click on dim gray color.	Click on any color you like from the color panel. I will choose dim gray.
Cursor on the panel.	Observe the panel. The color of the surface is now changed to dim gray. Close the dialog box.
Click on file menu.	Save image using Save Image option in the File menu.
Slide Number 7 Summary	Let's summarize. In this tutorial we have learnt to Show Amino acid hydrophobicity surface and Electrostatic Potential surface for protein and DNA structures. Create high quality images for publication using different viewing settings.
Slide Number 8 Assignment.	Now for the assignment: Show amino acid hydrophobicity surface and electrostatic potential surface for the structure of human hemoglobin (pdb code: 2dn1). Color the hem ligand green. Your completed assignment should look as follows.
Slide Number 9 Acknowledgement	The video at the following link summarizes the Spoken Tutorial project. Please download and watch it.
Slide Number 10 Acknowledgement	The Spoken Tutorial Project Team conducts workshops and gives certificates for those who pass an online test. For more details, please write to us.
Slide number 11 Acknowledgement	Spoken Tutorial Project is funded by NMEICT, MHRD, Government of India. More information on this Mission is available at the link shown
	This is Snehalatha from IIT Bombay signing off. Thank you for joining.

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Snehalathak