UCSF-Chimera/C4/Animation/English-timed
From Script | Spoken-Tutorial
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| 00:01 | Welcome to this tutorial on Animation using Chimera Interface. |
| 00:06 | In this tutorial, we will learn to : adjust background lighting and effects, |
| 00:12 | create scenes for animation, |
| 00:15 | place scenes along a timeline, |
| 00:17 | record a movie of the resulting animation. |
| 00:22 | To follow this tutorial, you should be familiar with Chimera interface. If not, for relevant tutorials, please visit our website. |
| 00:33 | To record this tutorial, I am using : Ubuntu OS version 14.04, Chimera version 1.10.2, Mozilla firefox browser 42.0 and a working internet connection. |
| 00:50 | Here I have opened Chimera window. |
| 00:53 | On the command text box, type: Open 1MBO. Press Enter. |
| 01:00 | A structure of hemoglobin opens on the panel. |
| 01:04 | Type: delete solvent to delete water molecules. Press Enter. |
| 01:10 | Let me demonstrate how to create a scene for Animation. |
| 01:15 | A Chimera scene can have - orientations of models and clipping planes, display styles and colors of models, molecular surfaces, electron density maps and electrostatic potential maps. |
| 01:33 | A scene can also have- 2D labels, axis, plane and centroid representation, CAST-P pocket display, parameters such as background lighting and effects. |
| 01:49 | Back to the panel. |
| 01:51 | Before we begin to create scenes for animation, let us learn to control background lighting. |
| 01:59 | Click on Tools menu, scroll down to Viewing Controls. From the sub-menu, select Effects. |
| 02:08 | Viewing dialog-box opens. |
| 02:11 | In the Effects section, click on depth cueing. |
| 02:16 | It refers to front-to-back shading. |
| 02:20 | Click on color well. |
| 02:22 | Choose a color for shading from the color well. |
| 02:26 | Close the color editor. |
| 02:29 | Click on Silhouettes to show outlines. |
| 02:33 | You can increase or decrease the width of the Silhouettes using Width field. |
| 02:39 | Click on color well. |
| 02:41 | Choose a color from the color editor. |
| 02:45 | Close the color editor. |
| 02:47 | Now click on Lighting button on the Viewing dialog box. |
| 02:51 | Here, we can change the lighting parameters according to requirement. |
| 02:57 | Click on Shininess button. |
| 03:00 | There are two options Intensity and Shininess. |
| 03:04 | Select Intensity. |
| 03:07 | Click on mode button. |
| 03:10 | By default, two-point lighting is selected. |
| 03:14 | Change it to three-point for more brightness. |
| 03:18 | Drag the slider to adjust brightness and contrast. |
| 03:23 | Again, click on Intensity button , choose Shininess. |
| 03:28 | Drag the slider to adjust sharpness and reflectivity. |
| 03:33 | Click on Save, then click on Close. |
| 03:37 | Rotate the structure on the panel. |
| 03:40 | Observe the Shading and Silhouettes. |
| 03:43 | Let us now create some scenes for animation. |
| 03:47 | Click on Tools menu, scroll down to Utilities option. |
| 03:52 | Click on Animation from the sub-menu. |
| 03:55 | Animation dialog-box opens. |
| 03:58 | Animation dialog-box has Scenes, Actions and Timeline sections. |
| 04:06 | Click on the green plus icon in the Scenes section. |
| 04:11 | This saves the current image on the panel as a scene. |
| 04:15 | It also generates a thumbnail image of the Scene, in the Scenes section. |
| 04:21 | This image is the first scene for animation. |
| 04:25 | Right-click on the thumbnail image, a context menu opens with options such as- Add to timeline, properties, delete etc. |
| 04:39 | Modify the display of the protein structure on the panel to create another Scene. |
| 04:45 | Using Presets menu, change the display to Interactive 1. |
| 04:50 | Select the ligand from Select menu. |
| 04:54 | From Actions menu, choose Sphere. This will change the ligand to CPK display. |
| 05:03 | Clear the selection. |
| 05:06 | In the Animation dialog box, click the green plus icon from the scenes section. |
| 05:12 | This will add the image on the panel as scene 2. |
| 05:16 | For scene 3 add axes for the helices present in the structure. |
| 05:22 | Click on Tools menu. Scroll down to Structure Analysis option. |
| 05:28 | Click on Axes, Planes, Centroids from the sub-menu. |
| 05:32 | In the Structure measurement dialog box , click on Define Axes. |
| 05 :37 | In the Define Axes dialog box, click on Each helix radio button. |
| 05:43 | Click on OK. |
| 05:47 | Add this image as scene 3. |
| 05:50 | Click on the plus icon in the Animation dialog-box. |
| 05:55 | Now, delete the axes. |
| 05:58 | In the Structure measurement dialog box, select all the rows. |
| 06:02 | Click on Delete button. |
| 06:05 | Close the Structure measurement dialog box. |
| 06:08 | For scene 4, select main using Select menu. |
| 06:15 | Show the surface using Actions menu. |
| 06:17 | Again select main from the Select menu. |
| 06:21 | Change the color of the surface to yellow using Actions menu. |
| 06:26 | Select Ligand and change the color of the ligand to blue. |
| 06:32 | Clear the selection. |
| 06:35 | Add this scene as scene 4 on the Animation dialog-box. |
| 06:40 | To show the substrate pocket more clearly, make the surface transparent. |
| 06:46 | Click on Actions menu, scroll down to surface. |
| 06:50 | From the sub-menu, choose transparency. Click on 50%. |
| 06:58 | Add this scene as 5th scene on the Scenes section. |
| 07:03 | If you want to delete a scene from the Scenes section, |
| 07:07 | right-click on the thumbnail image, select Delete option. |
| 07:13 | To add a scene, again click on plus icon. |
| 07:18 | Insert the scenes on Timeline section by drag and drop method using mouse button. |
| 07:25 | Click on thumbnail image, drag and place the image on the timeline. |
| 07:32 | Release the mouse button. |
| 07:34 | Alternatively, we can right-click on the thumbnail. |
| 07:38 | Select add to timeline option from contextmenu. |
| 07:43 | Add all the scenes to the Timeline in a sequence. |
| 07:47 | In the Actions section, there are 2 options; |
| 07:51 | Rock- for oscillating motion. Roll- for continuous motion. |
| 07:57 | Let us choose Roll. |
| 07:59 | Now we are ready to record this animation. |
| 08:03 | Click on Record button. |
| 08:06 | Record animation dialog-box opens. |
| 08:13 | I will choose Desktop to save the file. Give a file name in the File name text box. |
| 08:17 | Type the file name as Animation hyphen one (Animation-1). |
| 08:21 | Select file type as .ogv or any movie format of your choice. |
| 08:28 | Click on Record button to start recording the animation. |
| 08:33 | The series of images will be encoded into a movie file on the desktop. |
| 08:42 | If you want to abort the recording process- click on the Record button again, on the Animation dialog box. |
| 08:49 | It will take a few minutes to complete the recording process. |
| 08:54 | The file will be saved as Animation hyphen one (Animation-1) on the desktop. |
| 09:01 | Double-click on the .ogv file to view the animation. |
| 09:14 | Let's summarize. In this tutorial, we have learnt to: adjust background lighting and effects, create scenes for animation, |
| 09:23 | Place scenes along a Timeline. Record a movie of the resulting animation. |
| 09:30 | As an assignment, open a model of Chymotrypsin (PDB code: 7GCH). |
| 09:35 | Adjust background and lighting effects. |
| 09:38 | Adjust transparency to show ligand inside the protein surface. |
| 09:43 | Create a few scenes and make animation movie. |
| 09:47 | This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it. |
| 09:55 | We conduct workshops using Spoken Tutorials and give certificates. Please contact us. |
| 10:03 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
| 10:09 | This is Snehalatha from IIT Bombay, signing off.
Thank you for joining. |
