Difference between revisions of "UCSF-Chimera/C4/Animation/English-timed"
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− | | In this tutorial, we will learn to : | + | | In this tutorial, we will learn to : adjust background lighting and effects, |
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|00:12 | |00:12 | ||
− | | | + | | create scenes for '''animation''', |
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|00:15 | |00:15 | ||
− | | | + | | place scenes along a '''timeline''', |
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|00:17 | |00:17 | ||
− | | | + | | record a movie of the resulting <br/> '''animation'''. |
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|00:22 | |00:22 | ||
− | | To follow this tutorial you should be familiar with | + | | To follow this tutorial, you should be familiar with '''Chimera''' interface. If not, for relevant tutorials, please visit our '''website'''. |
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|00:33 | |00:33 | ||
− | | To record this tutorial, I am using : '''Ubuntu''' | + | | 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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− | | On the command text box type '''Open 1MBO.''' Press '''Enter'''. | + | | On the '''command''' text box, type: '''Open 1MBO.''' Press '''Enter'''. |
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− | | Type | + | | Type: '''delete solvent''' to delete water molecules. Press '''Enter'''. |
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|01:10 | |01:10 | ||
− | | Let me demonstrate how to create a ''' | + | | Let me demonstrate how to create a '''scene''' for '''Animation'''. |
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| 01:15 | | 01:15 | ||
− | | A '''Chimera scene''' can have - | + | | 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. |
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|01:33 | |01:33 | ||
− | | A | + | | 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 | ||
− | | Click on | + | | Click on '''Tools''' menu, scroll down to '''Viewing Controls.''' From the sub-menu, select '''Effects'''. |
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− | | In the '''Effects''' section click on '''depth cueing.''' | + | | In the '''Effects''' section, click on '''depth cueing.''' |
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− | |Here we can change the lighting parameters | + | |Here, we can change the lighting parameters according to requirement. |
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− | | By default '''two-point''' lighting is selected. | + | | By default, '''two-point''' lighting is selected. |
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|03:18 | |03:18 | ||
− | | Drag the slider to adjust '''brightness '''and '''contrast'''. | + | | Drag the '''slider''' to adjust '''brightness '''and '''contrast'''. |
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| 03:23 | | 03:23 | ||
− | | Again, | + | | Again, click on '''Intensity''' button , choose '''Shininess'''. |
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|03:28 | |03:28 | ||
− | |Drag the slider | + | |Drag the slider to adjust '''sharpness''' and '''reflectivity'''. |
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|03:33 | |03:33 | ||
− | | 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 | + | | Let us now create some scenes for animation. |
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− | | Click on the green | + | | Click on the green plus icon in the '''Scenes''' section. |
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|04:11 | |04:11 | ||
− | |This | + | |This '''save'''s the current '''image''' on the panel as a '''scene'''. |
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|04:15 | |04:15 | ||
− | |It also generates a '''thumbnail image''' of the | + | |It also generates a '''thumbnail image''' of the '''Scene''', in the '''Scenes''' section. |
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− | | Right-click on the '''thumbnail''' image, a '''context menu''' opens with options such as | + | | Right-click on the '''thumbnail''' image, a '''context menu''' opens with options such as- '''Add to timeline,''' '''properties''', '''delete '''etc. |
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|04:54 | |04:54 | ||
− | |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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− | | In the''' Animation '''dialog box, click the green | + | | In the''' Animation '''dialog box, click the green plus icon from the '''scenes''' section. |
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− | | In the '''Structure measurement | + | | In the '''Structure measurement''' dialog box , click on '''Define Axes'''. |
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− | |Click on the | + | |Click on the plus icon in the '''Animation''' dialog-box. |
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|05:55 | |05:55 | ||
− | | Now delete the '''axes'''. | + | | Now, delete the '''axes'''. |
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| 05:58 | | 05:58 | ||
− | |In the '''Structure measurement | + | |In the '''Structure measurement''' dialog box, select all the rows. |
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− | |Close the '''Structure measurement | + | |Close the '''Structure measurement''' dialog box. |
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Revision as of 17:08, 28 June 2018
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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. |