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

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Latest revision as of 19:31, 30 September 2016

Visual Cue
Narration
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
  • Adjust background lighting and effects.
  • Create scenes for animation.
  • Place scenes along a timeline.
  • Record a movie of the resulting
    animation.


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
  • Ubuntu OS version. 14.04
  • Chimera version 1.10.2
  • Mozilla firefox browser 42.0
  • And a working Internet connection.


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.


Press Enter.

Cursor on the panel. A structure of hemoglobin opens on the panel.
Cursor on the command line. Type, delete solvent to delete water molecules.


Press Enter.

Cursor on the panel. Let me demonstrate how to create a scenes for Animation.
Slide Number 5

Scenes

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.
Slide Number 6

Scenes

A Scene can also have-
  • 2D labels.
  • Axis, plane and centroid representation.
  • CAST-P pocket display.
  • Parameters such as background lighting and effects.
Click on tools menu, scroll down to viewing controls. Back to the panel.


Before we begin to create scenes for animation, let us learn to control background lighting.

Click on Effects. Click on tools menu, scroll down to Viewing Controls.


From the sub-menu select Effects.


Viewing dialog-box opens.

Cursor on the Viewing dialog-box. In the Effects section click on depth cueing.


It refers to front-to-back shading.

Click on the color well.


Click on color well.


Choose a color for shading from the color well.


Close the color editor.

Click on Silhouettes. Click on Silhouettes to show outlines.


You can increase or decrease the width of the Silhouettes using Width field.

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.


Here we can change the lighting parameters, according to requirement.

Click on intensity button.


Click on mode button.

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.


Drag the slider to adjust sharpness and reflectivity.

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.


Observe the Shading and Silhouettes.

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.


Click on Animation from the sub-menu.

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.


This saves the current image on the panel as a scene.


It also generates a thumbnail image of the Scene in the Scenes section.

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;


Add to timeline, properties, delete etc.

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.


From Actions menu choose Sphere.


This will change the ligand to CPK display.

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.


This will add the image on the panel as scene 2.

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.


Click on Axes, Planes and Centroids.

Click on Tools menu. Scroll down to Structure Analysis option.


Click on Axes, Planes, Centroids from the sub-menu.

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.


In the Define Axes dialog box, click on Each helix radio button.

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.


Click on Delete button.

Now delete the axes.


In the Structure measurement dialog box, select all the rows.


Click on Delete button.


Close the Structure measurement dialog box.

Click Select menu, scroll down to Structure.


For scene 4, select main using Select menu.


Show the surface using Actions menu.

Choose main from the sub-menu.


Click on the Actions menu, select Surface, click on Show.

Again select main from the Select menu.


Change the color of the surface to yellow using Actions menu.


Select Ligand and change the color of the ligand to blue.


Clear the selection.

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.


Click on Surface, Transparency select 50%.


To show the substrate pocket more clearly, make the surface transparent.


Click on Actions menu, scroll down to surface.


From the sub-menu choose transparency. Click on 50%.

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;


Right-click on the thumbnail image, select delete option.


To add a scene, again click on plus icon.

Drag and drop the scenes on the Timeline.


Insert the scenes on Timeline section, by drag and drop method using mouse button.


Click on thumbnail image, drag and place the image on the timeline.


Release the mouse button.

Right-click on the thumbnail and select add to timeline option Alternatively we can right-click on the thumbnail.


Select add to timeline option from contextmenu.

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.


Now we are ready to record this animation.

Click on Record button.


Click on Record button.


Record animation dialog-box opens.

Click on desktop.


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.


Type the file name as Animation hyphen one (Animation-1).


Select file type as .ogv or any movie format of your choice.

Click on Record button in the Record Animation dialog-box.


Click on Record button to start recording the animation.


The series of images will be encoded into a movie file on the desktop.

Click on Record button in the Animation dialog-box. If you want to abort the recording process;


Click on the Record button again on the Animation dialog box.

Cursor on the panel. It will take a few minutes to complete the recording process.


The file will be saved as Animation hyphen one (Animation-1) on the desktop.

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

  • Adjust background lighting and effects.
  • Create scenes for animation.
  • Place scenes along a Timeline.
  • Record a movie of the resulting
    animation.


Slide Number 8

Assignment

As an assignment
  • Open a model of Chymotrypsin (PDB code: 7GCH).
  • Adjust background and lighting effects.
  • Adjust transparency to show ligand inside the protein surface.
  • Create a few scenes and make animation movie.
Slide Number 9

Acknowledgement

* This video summarizes the Spoken Tutorial project
  • If you do not have good bandwidth, you can download and watch it.


Slide Number 10 * We conduct workshops using Spoken Tutorials and give certificates.
  • Please contact us.


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.

Contributors and Content Editors

Nancyvarkey, Snehalathak

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