UCSF-Chimera/C4/Animation/English-timed - Revision history

Sandhya.np14 at 12:11, 28 June 2018

2018-06-28T12:11:01Z

Sandhya.np14 at 12:10, 28 June 2018

2018-06-28T12:10:13Z

Sandhya.np14 at 11:38, 28 June 2018

2018-06-28T11:38:53Z

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Jyotisolanki: Created page with "{| border=1 | Time | Narration |- | 00:01 | Welcome to this tutorial on '''Animation '''using''' Chimera Interface.''' |- |00:06 | In thi..."

2017-12-13T10:46:00Z

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..."

New page

{| border=1
| <center>Time</center>
| <center>Narration</center>

|-
| 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 <br/> '''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 '''scenes''' 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 S'''cene''' 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 '''5<sup>th</sup> 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 '''context'''menu.

|-
|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 <br/> '''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.

|}

@@ Line 21: / Line 21: @@
 |-
 |00:17
-| record a movie of the resulting <br/> '''animation'''.
+| record a movie of the resulting '''animation'''.
 |-

@@ Line 317: / Line 317: @@
 |-
 |06:40
-|  To show the substrate pocket''' '''more clearly, make the surface transparent.
+|  To show the '''substrate pocket''' more clearly, make the surface transparent.
 |-
@@ Line 325: / Line 325: @@
 |-
 |06:50
-|From the sub-menu choose '''transparency.''' Click on 50%.
+|From the sub-menu, choose '''transparency.''' Click on '''50%'''.
 |-
 |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
-|  If you want to delete a scene from the '''Scenes section;'''
+|  If you want to delete a scene from the '''Scenes''' section,
 |-
 |07:07
-|Right-click on the '''thumbnail''' image, select delete option.
+|right-click on the '''thumbnail''' image, select '''Delete''' option.
 |-
 |07:13
-|To add a scene, again click on '''plus''' icon.
+|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.
+|  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'''.
+|Click on '''thumbnail''' image, drag and place the '''image''' on the '''timeline'''.
 |-
 |07:32
-|Release the mouse button.
+|Release the '''mouse''' button.
 |-
 |07:34
-|  Alternatively we can right-click on the '''thumbnail'''.
+|  Alternatively, we can right-click on the '''thumbnail'''.
 |-
@@ Line 369: / Line 369: @@
 |-
 |07:47
-|  In the Actions section there are 2 options;
+|  In the '''Actions''' section, there are 2 options;
 |-
@@ Line 381: / Line 381: @@
 |-
 |07:59
-|Now we are ready to record this animation.
+|Now we are ready to '''record''' this animation.
 |-
@@ Line 393: / Line 393: @@
 |-
 |08:13
-|  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
-|  Type the file name as '''Animation hyphen one '''('''Animation-1).'''
+|  Type the file name as '''Animation hyphen one '''(Animation-1).
 |-
 |08:21
-|Select file type as''' .ogv''' or any movie format of your choice.
+|Select file type as''' .ogv''' or any '''movie format''' of your choice.
 |-
@@ Line 409: / Line 409: @@
 |-
 |08:33
-|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
-|  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.
 |-
@@ Line 429: / Line 429: @@
 |-
 |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
-| 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
-|  As an assignment Open a model of '''Chymotrypsin (PDB code: 7GCH''').
+|  As an assignment, open a model of '''Chymotrypsin (PDB code: 7GCH''').
 |-
@@ Line 453: / Line 453: @@
 |-
 |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.
 |-
@@ Line 461: / Line 461: @@
 |-
 |10:03
-|  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
-|  This is Snehalatha from IIT Bombay signing off.
+|  This is Snehalatha from IIT Bombay, signing off.
-−
 Thank you for joining.
 |}