UCSF-Chimera/C4/Animation/English
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Slide Number 1
Title Slide |
Welcome to this tutorial on Animation using Chimera Interface. |
Slide Number 2
Learning Objectives |
In this tutorial, we will learn to
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Slide Number 3
Pre-requisites |
To follow this tutorial you should be familiar with,
Chimera Interface. If not, for relevant tutorials, please visit our website. |
Slide Number 4
System Requirement |
To record this tutorial, I am using
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Double-click on Chimera icon. | Here I have opened Chimera window. |
On the command text box type 1MBO. | On the command text box type Open 1MBO.
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Cursor on the panel. | A structure of hemoglobin opens on the panel. |
Cursor on the command line. | Type, delete solvent to delete water molecules.
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Cursor on the panel. | Let me demonstrate how to create a scenes for Animation. |
Slide Number 5
Scenes |
A Chimera scene can have -
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Slide Number 6
Scenes |
A Scene can also have-
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Click on tools menu, scroll down to viewing controls. | Back to the panel.
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Click on Effects. | Click on tools menu, scroll down to Viewing Controls.
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Cursor on the Viewing dialog-box. | In the Effects section click on depth cueing.
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Click on the color well.
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Click on color well.
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Click on Silhouettes. | Click on Silhouettes to show outlines.
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Click on color well.
Drag the slider to select a color. Close the color editor. |
Click on color well.
Choose a color from the color editor. Close the color editor. |
Click on Lighting button. | Now click on Lighting button on the Viewing dialog box.
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Click on intensity button.
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Click on Shininess button.
There are two options Intensity and Shininess. Select Intensity. Click on mode button. |
Select three-point. | By default two-point lighting is selected.
Change it to three-point for more brightness. |
Drag the slider for brightness and contrast | Drag the slider to adjust brightness and contrast. |
Click on the intensity button and choose Shininess.
Drag the slider to adjust sharpness and reflectivity. |
Again, Click on Intensity button , choose Shininess.
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Click on Save then click on close. | Click on Save then click on Close. |
Using mouse button rotate the structure. | Rotate the structure on the panel.
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Cursor on the panel. | Let us now create some scenes for animation. |
Click on Tools menu, scroll down to Utilities option.
Click on Animation from the sub-menu. |
Click on Tools menu, scroll down to Utilities option.
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Cursor on the Animation dialog box. | Animation dialog-box opens. |
Cursor on Chimera Window. | Animation dialog-box has Scenes, Actions and Timeline sections. |
Click on the green plus icon in the scenes section. | Click on the green plus icon in the Scenes section.
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Cursor on the panel. | This image is the first scene for animation. |
Right-click on the scene thumbnail. | Right-click on the thumbnail image, a context menu opens with options such as;
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Cursor on the panel. | Modify the display of the protein structure on the panel to create another Scene. |
Click on Presets menu. Select interactive 1. | Using Presets menu, change the display to Interactive 1. |
Click on Select menu, select ligand.
Scroll down the actions menu. Select Spheres. |
Select the ligand from Select menu.
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Scroll down the Select menu. | Clear the selection. |
Click the green plus icon on the scenes section of Animation dialog box. | In the Animation dialog box, click the green plus icon from the scenes section.
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Cursor on the panel. | For scene 3 add axes for the helices present in the structure. |
Click on tools menu. Scroll down to Structure Analysis option.
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Click on Tools menu. Scroll down to Structure Analysis option.
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In the Structure measurement dialog box , click on Define Axes.
In the Define Axes dialog box, click on Each helix radio button. |
In the Structure measurement dialog box , click on Define Axes.
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Click on OK button. | Click on OK. |
Click the plus icon on the scenes section of Animation dialog box. | Add this image as scene 3.
Click on the plus icon in the Animation dialog-box. |
In the Structure measurement dialog box, select all the rows.
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Now delete the axes.
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Click Select menu, scroll down to Structure.
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For scene 4, select main using Select menu.
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Choose main from the sub-menu.
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Again select main from the Select menu.
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Click on the green plus icon in the scenes section. | Add this scene as scene 4 on the Animation dialog-box. |
Click on Actions menu, scroll down to surface.
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To show the substrate pocket more clearly, make the surface transparent.
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Click on the green plus icon in the scenes section. | Add this scene as 5th scene on the scenes section. |
Right-click on the thumbnail, and select delete option. | If you want to delete a scene from the Scenes section;
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Drag and drop the scenes on the Timeline.
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Insert the scenes on Timeline section, by drag and drop method using mouse button.
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Right-click on the thumbnail and select add to timeline option | Alternatively we can right-click on the thumbnail.
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Cursor on the Animation dialog box. | Add all the scenes to the Timeline in a sequence. |
Cursor on the Animation dialog box. | In the Actions section there are 2 options;
Rock- for oscillating motion Roll- for continuous motion. |
Click on Roll from the Action section. | Let us choose Roll.
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Click on Record button.
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Click on Record button.
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Click on desktop.
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I will choose Desktop to save the file.
Give a file name in the File name text box. |
Type the file name as Animation-1 in the file name text box.
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Type the file name as Animation hyphen one (Animation-1).
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Click on Record button in the Record Animation dialog-box.
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Click on Record button to start recording the animation.
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Click on Record button in the Animation dialog-box. | If you want to abort the recording process;
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Cursor on the panel. | It will take a few minutes to complete the recording process.
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Double-click on Animation-1.ogv on the desktop. | Double-click on the .ogv file to view the animation. |
Slide Number 7
Summary |
Let's summarize,
In this tutorial we have learnt to
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Slide Number 8
Assignment |
As an assignment
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Slide Number 9
Acknowledgement |
* This video summarizes the Spoken Tutorial project
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Slide Number 10 | * We conduct workshops using Spoken Tutorials and give certificates.
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Slide number 11 | The Spoken Tutorial Project is funded by NMEICT, MHRD Government of India. |
This is Snehalatha from IIT Bombay signing off.
Thank you for joining. |