UCSF-Chimera/C4/Animation/English-timed

Time	Narration
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.

Contributors and Content Editors

Jyotisolanki, Sandhya.np14