Difference between revisions of "UCSF-Chimera/C4/Animation/English-timed"

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(Created page with "{| border=1 | <center>Time</center> | <center>Narration</center> |- | 00:01 | Welcome to this tutorial on '''Animation '''using''' Chimera Interface.''' |- |00:06 | In thi...")
 
 
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|-
 
|-
 
|00:06
 
|00:06
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|  In this tutorial, we will learn to : Adjust '''background lighting''' and '''effects'''.
+
|  In this tutorial, we will learn to : adjust background lighting and effects,
  
 
|-
 
|-
 
|00:12
 
|00:12
−
| Create '''scenes''' for '''animation'''.
+
| create scenes for '''animation''',
  
 
|-
 
|-
 
|00:15
 
|00:15
−
| Place '''scenes''' along a '''timeline'''.
+
| place scenes along a '''timeline''',
  
 
|-
 
|-
 
|00:17
 
|00:17
−
| Record a movie of the resulting <br/> '''animation'''.
+
| record a movie of the resulting '''animation'''.
  
 
|-
 
|-
 
|00:22
 
|00:22
−
| To follow this tutorial you should be familiar with, '''Chimera''' Interface. If not, for relevant tutorials, please visit our website.  
+
| To follow this tutorial, you should be familiar with '''Chimera''' interface. If not, for relevant tutorials, please visit our '''website'''.  
  
 
|-
 
|-
 
|00:33
 
|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.
+
|  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.
  
 
|-
 
|-
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|-
 
|-
 
|00:53
 
|00:53
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|  On the command text box type '''Open 1MBO.'''  Press '''Enter'''.
+
|  On the '''command''' text box, type: '''Open 1MBO.'''  Press '''Enter'''.
  
 
|-
 
|-
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|-
 
|-
 
|01:04
 
|01:04
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|  Type, '''delete solvent''' to delete water molecules. Press '''Enter'''.
+
|  Type: '''delete solvent''' to delete water molecules. Press '''Enter'''.
  
 
|-
 
|-
 
|01:10
 
|01:10
−
|  Let me demonstrate how to create a '''scenes''' for '''Animation'''.
+
|  Let me demonstrate how to create a '''scene''' for '''Animation'''.
  
 
|-
 
|-
 
| 01:15
 
| 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.
+
|  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
 
|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.
+
|  A scene can also have- 2D labels, axis, plane and centroid representation, CAST-P pocket display, parameters such as background lighting and effects.
  
 
|-
 
|-
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|-
 
|-
 
|01:59
 
|01:59
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|  Click on tools menu, scroll down to '''Viewing Controls ''' From the sub-menu select '''Effects'''.
+
|  Click on '''Tools''' menu, scroll down to '''Viewing Controls.''' From the sub-menu, select '''Effects'''.
  
 
|-
 
|-
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|-
 
|-
 
| 02:11
 
| 02:11
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|  In the '''Effects''' section click on '''depth cueing.'''
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|  In the '''Effects''' section, click on '''depth cueing.'''
  
 
|-
 
|-
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|-
 
|-
 
|02:51  
 
|02:51  
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|Here we can change the lighting parameters, according to requirement.
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|Here, we can change the lighting parameters according to requirement.
  
 
|-
 
|-
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|-
 
|-
 
|03:10
 
|03:10
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|  By default '''two-point''' lighting is selected.
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|  By default, '''two-point''' lighting is selected.
  
 
|-
 
|-
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|-
 
|-
 
|03:18
 
|03:18
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|  Drag the slider to adjust '''brightness '''and '''contrast'''.  
+
|  Drag the '''slider''' to adjust '''brightness '''and '''contrast'''.  
  
 
|-
 
|-
 
| 03:23
 
| 03:23
−
|  Again, Click on '''Intensity''' button , choose '''Shininess'''.
+
|  Again, click on '''Intensity''' button , choose '''Shininess'''.
  
 
|-
 
|-
 
|03:28  
 
|03:28  
−
|Drag the slider''' '''to adjust '''sharpness''' and '''reflectivity'''.  
+
|Drag the slider to adjust '''sharpness''' and '''reflectivity'''.  
  
 
|-
 
|-
 
|03:33  
 
|03:33  
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|  Click on '''Save''' then click on '''Close.'''  
+
|  Click on '''Save''', then click on '''Close.'''  
  
 
|-
 
|-
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|-
 
|-
 
|03:43  
 
|03:43  
−
|  Let us now create some '''scenes''' for '''animation.'''
+
|  Let us now create some scenes for animation.
  
 
|-
 
|-
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|-
 
|-
 
|04:06  
 
|04:06  
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|  Click on the green '''plus icon''' in the '''Scenes''' section.
+
|  Click on the green plus icon in the '''Scenes''' section.
  
 
|-
 
|-
 
|04:11
 
|04:11
−
|This saves the current image on the panel as a '''scene'''.
+
|This '''save'''s the current '''image''' on the panel as a '''scene'''.
  
 
|-
 
|-
 
|04:15
 
|04:15
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|It also generates a '''thumbnail image''' of the S'''cene''' in the '''Scenes''' section.
+
|It also generates a '''thumbnail image''' of the '''Scene''', in the '''Scenes''' section.
  
 
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|-
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|-
 
|-
 
|04:25
 
|04:25
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|  Right-click on the '''thumbnail''' image, a '''context menu''' opens with options such as; '''Add to timeline,''' '''properties''', '''delete '''etc.
+
|  Right-click on the '''thumbnail''' image, a '''context menu''' opens with options such as- '''Add to timeline,''' '''properties''', '''delete '''etc.
  
 
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|-
 
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|04:54
 
|04:54
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|From '''Actions''' menu choose '''Sphere.''' This will change the '''ligand''' to '''CPK''' display.
+
|From '''Actions''' menu, choose '''Sphere.''' This will change the '''ligand''' to '''CPK''' display.
  
 
|-
 
|-
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|-
 
|-
 
|05:06
 
|05:06
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|  In the''' Animation '''dialog box, click the green '''plus''' icon from the '''scenes''' section.
+
|  In the''' Animation '''dialog box, click the green plus icon from the '''scenes''' section.
  
 
|-
 
|-
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|-
 
|-
 
|05:32
 
|05:32
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|  In the '''Structure measurement dialog box''' , click on '''Define Axes'''.
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|  In the '''Structure measurement''' dialog box , click on '''Define Axes'''.
  
 
|-
 
|-
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|-
 
|-
 
|05:50
 
|05:50
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|Click on the '''plus''' icon in the '''Animation''' dialog-box.
+
|Click on the plus icon in the '''Animation''' dialog-box.
  
 
|-
 
|-
 
|05:55
 
|05:55
−
|  Now delete the '''axes'''.
+
|  Now, delete the '''axes'''.
  
 
|-
 
|-
 
| 05:58
 
| 05:58
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|In the '''Structure measurement dialog box''', select all the rows.  
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|In the '''Structure measurement''' dialog box, select all the rows.  
  
 
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|-
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|06:05
 
|06:05
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|Close the '''Structure measurement dialog box'''.
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|Close the '''Structure measurement''' dialog box.
  
 
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|-
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|06:40  
 
|06:40  
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|  To show the substrate pocket''' '''more clearly, make the surface transparent.
+
|  To show the '''substrate pocket''' more clearly, make the surface transparent.
  
 
|-
 
|-
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|-
 
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|06:50
 
|06:50
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|From the sub-menu choose '''transparency.''' Click on 50%.  
+
|From the sub-menu, choose '''transparency.''' Click on '''50%'''.  
  
 
|-
 
|-
 
|06:58  
 
|06:58  
−
|  Add this scene as '''5<sup>th</sup> scene''' on the scenes section.
+
|  Add this scene as '''5<sup>th</sup> scene''' on the '''Scenes''' section.
  
 
|-
 
|-
 
|07:03  
 
|07:03  
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|  If you want to delete a scene from the '''Scenes section;'''
+
|  If you want to delete a scene from the '''Scenes''' section,
  
 
|-
 
|-
 
|07:07
 
|07:07
−
|Right-click on the '''thumbnail''' image, select delete option.  
+
|right-click on the '''thumbnail''' image, select '''Delete''' option.  
  
 
|-
 
|-
 
|07:13  
 
|07:13  
−
|To add a scene, again click on '''plus''' icon.
+
|To add a scene, again click on plus icon.
  
 
|-
 
|-
 
|07:18
 
|07:18
−
|  Insert the scenes on '''Timeline section''', by drag and drop method using mouse button.
+
|  Insert the scenes on '''Timeline''' section by drag and drop method using '''mouse button'''.
  
 
|-
 
|-
 
|07:25
 
|07:25
−
|Click on '''thumbnail''' image, drag and place the image on the '''timeline'''.
+
|Click on '''thumbnail''' image, drag and place the '''image''' on the '''timeline'''.
  
 
|-
 
|-
 
|07:32
 
|07:32
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|Release the mouse button.
+
|Release the '''mouse''' button.
  
 
|-
 
|-
 
|07:34
 
|07:34
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|  Alternatively we can right-click on the '''thumbnail'''.
+
|  Alternatively, we can right-click on the '''thumbnail'''.
  
 
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|07:47  
 
|07:47  
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|  In the Actions section there are 2 options;
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|  In the '''Actions''' section, there are 2 options;
  
 
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|07:59
 
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|Now we are ready to record this animation.
+
|Now we are ready to '''record''' this animation.
  
 
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|08:13
 
|08:13
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|  I will choose '''Desktop''' to save the file. Give a file name in the '''File name''' text box.
+
|  I will choose '''Desktop''' to '''save''' the file. Give a file name in the '''File name''' text box.
  
 
|-
 
|-
 
|08:17  
 
|08:17  
−
|  Type the file name as '''Animation hyphen one '''('''Animation-1).'''
+
|  Type the file name as '''Animation hyphen one '''(Animation-1).
  
 
|-
 
|-
 
|08:21  
 
|08:21  
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|Select file type as''' .ogv''' or any movie format of your choice.
+
|Select file type as''' .ogv''' or any '''movie format''' of your choice.
  
 
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|08:33
 
|08:33
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|The series of images will be encoded into a movie file on the desktop.
+
|The series of images will be encoded into a '''movie file''' on the desktop.
  
 
|-
 
|-
 
|08:42  
 
|08:42  
−
|  If you want to abort the recording process; Click on the '''Record''' button again on the '''Animation''' dialog box.
+
|  If you want to abort the recording process- click on the '''Record''' button again, on the '''Animation''' dialog box.
  
 
|-
 
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|-
 
|-
 
|09:14
 
|09:14
−
|  Let's summarize, In this tutorial we have learnt to  Adjust '''background lighting''' and '''effects'''. Create '''scenes''' for '''animation'''.
+
|  Let's summarize. In this tutorial, we have learnt to: adjust '''background lighting''' and '''effects''', create '''scenes''' for '''animation''',
  
 
|-
 
|-
 
|09:23
 
|09:23
−
| Place scenes along a '''Timeline'''.  Record a movie of the resulting <br/> '''animation'''.
+
| Place scenes along a '''Timeline'''.  Record a movie of the resulting '''animation'''.
  
 
|-
 
|-
 
|09:30
 
|09:30
−
|  As an assignment Open a model of '''Chymotrypsin (PDB code: 7GCH''').
+
|  As an assignment, open a model of '''Chymotrypsin (PDB code: 7GCH''').
  
 
|-
 
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|09:47
 
|09:47
−
| This video summarizes the Spoken Tutorial project. If you do not have good bandwidth, you can download and watch it.
+
| This video summarizes the '''Spoken Tutorial''' project. If you do not have good bandwidth, you can download and watch it.
  
 
|-
 
|-
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|-
 
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|10:03  
 
|10:03  
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|  The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' '''Government of '''India.  
+
|  The Spoken Tutorial Project is funded by '''NMEICT, MHRD''' Government of India.  
  
 
|-
 
|-
 
|10:09
 
|10:09
−
|  This is Snehalatha from IIT Bombay signing off.  
+
|  This is Snehalatha from IIT Bombay, signing off.  
−
 
+
 
Thank you for joining.  
 
Thank you for joining.  
  
 
|}
 
|}

Latest revision as of 17:41, 28 June 2018

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

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