ProteinShader: General Controls

Keyboard Shortcuts

The keyboard controls listed below will only work if the drawing canvas has the focus. Clicking anywhere on the canvas will give it the focus.

Mouse Motion Control

The mouse can be dragged across the canvas to rotate an image or zoom the camera in or out. The mouse buttons for motion and camera control are explained in the table right below. The image can also be rotated at constant speed by using the Motion Panel described further down the page.

Many newer Macintosh OS X machines may have a two or three button mouse, in which case the button controls will likely be the same as for Linux and Windows XP. However, if only a single-button mouse is present, the shift and command keys will need to be used in combination with the mouse button, as indicated in the table.

For zooming the camera in or out with a center-drag (button two on a three button mouse), the drag should be vertical. If the mouse has a scroll wheel, that should also work for zooming the camera in or out. For rotating the image on the z-axis of the view, the right-button drag with the shift key held down should be horizontal.

When the window with the canvas has the focus (because it was clicked on), the camera can also be zoomed in or out by using keyboard shortcuts. The "i" key (upper or lowercase) will zoom the camera in by 5 angstroms, while the "o" key (upper or lowercase) will zoom the camera out by 5 ansgstroms.

Motion Panel

If the Motion subpanel is not already visible, select Motion from the menu at the top right of the retractable Control Panel on the right side of the ProteinShader GUI. When the Start button is clicked, the number of frames per second (fps) for the animation will be reported in the box at the bottom of the Motion subpanel, and also in red letters at the top left of the canvas.

The slider or text box for the Y-Axis can be used to specify the number of degrees per second of rotation about the protein structures's y-axis. Because the rotation speed is given in degrees per second, the speed will be about the same on different machines. However, how smooth or jerky the animation appears to be will depend on the number of frames per second that can be rendered, and that rendering speed will depend on both how complex the image is, and on how powerful the graphics card is. The X-Axis slider and text box set the degrees per second for the x-axis, with the subtle distinction that the rotation is about the x-axis of the view rather than the x-axis of the protein structure itself.

Antialiasing

The term aliasing refers to the jagged edges that are often produced when rendering geometrically defined objects (see part A of Figure 1 below for an example). Techniques for smoothing out these jagged edges are called antialiasing. Aliasing occurs because of the discrete nature of pixels [1], and because a pixel is detemined to be inside or outside of an object based on whether the center of the pixel falls within a mathematically calculated imaginary boundary line.

A

B

C

D

Figure 1. Application of antialiasing to a pen-and-ink style tubes display of the retinol-binding protein. (A) Halftoning image with no antialiasing. The 140 by 210 pixels image was taken from a monitor with a 72 pixels per inch resolution, where the aliasing (jagged edge) effect is quite noticeable against a white background. (B) The same as (A), except that the Antialiasing subpanel shown further below has been used to partially smooth out the black edges of halftoning images by adding gray pixels next to the edge lines. (C) The same as (B), except that additional antialiasing has been performed by jittering the entire scene 3 times and blending the images. (D) The same as (C), except that scene is jittered 6 times. The retinol-binding protein was loaded from file 1AQB.pdb [2, 3].

Antialiasing Panel

The Antialiasing subpanel of the ProteinShader GUI provides controls for smoothing out jagged edges in order to produce publication quality images.

• Entire Scene

  The checkbox and menu in the top half of the Antialiasing subpanel can be used to apply antialiasing by jittering the entire scene from 2 to 16 times and blending the images in an accumulation buffer (jittering means to move the image a fraction of a pixel each time it is rendered). The xy-coordinates used for jittering are taken from the OpenGL Programming Guide [4].

  Entire-scene antialising is primarily intended for smoothing out jagged edges right before saving images from the canvas as PNG or JPEG files. By default, the whole-scene antialiasing checkbox is not selected because rendering times may be dramatically slowed. If a scene is jittered n times, then rendering will take approximately n times longer, so jittering even 3 or 4 times might be unacceptably slow for an animation (constant rotation) unless a fairly high-end graphics card is being used. Jittering the entire scene may also slow down responsiveness to the GUI controls, so it is generally best to leave whole-scene antialiasing off while performing manipulations such as changing colors, visibility status, zooming in on an image, etc.

• Black edges of halftoning images

  When ribbons and tubes with halftoning (pen-and-ink style) are drawn against a white background, the darkened edges often appear to be quite jagged, as shown above in Figure 1A. If the checkbox in the bottom half of the Antialiasing panel is selected, the jagged edges are partially smoothed out by adding additional gray pixels outside of the black edges. This effect is accomplished by rendering a translucent black silhouette of each tube or ribbon segment before rendering with halftoning. The silhouette is drawn 4 times with a slightly offset (a half pixel up, down, left, or right).

  This silhouette-based antialiasing only affects halftoning images, not any of the color images. Rendering may be slowed down 2 to 3-fold, depending on the graphics card. By default, this type of antialiasing is turned on despite the performance cost. Without any antialiasing, rotating halftoning images against a white background can produce a very annoying kinetic effect at the darkened edges. However, it the Background menu above the canvas is used to change the background to black, the aliasing problem is less noticeable, so it may be ok to deselect the antialiasing option in order to speed up the frames per second for an animation.