ProteinShader: Atom Controls

Selection Panel

The selection subpanel can be seen on the left side of the control panel shown right below. The same selection panel is used for both Atom-style (spheres and cylinders) and Cartoon-style (tubes and ribbons) displays. There are four kinds of selections:

• Model

  If a protein structure is determined by magnetic resonance imaging (NMR), there will typically be several possible models in the Protein Data Bank file. The ProteinShader program will read in all of the models, and the model to display can be selected from the Model menu at the top left of the control panel. Models are normally designated by integers, starting at 1. If a protein structure is determined by x-ray crystallography, there will usually be only a single model.

• Chain

  A model will always have at least one polypeptide chain, and might have several. Chains are usually designated by uppercase letters, starting at A.

• Amino Acids, Heterogens, or Waters

  The menu right below the Chain menu can be used to select Amino Acids, Heterogens, or Water. The list below the menu will display the residues (the term residue is being used rather broadly to include heterogens and water because they are specified in a similar manner to amino acids in a PDB file). To select a continuous range of residues, hold down the shift key while using the mouse to left click list items. To select a discontinous range of residues, use the control key (command key on Macintosh OS X) instead of the shift key.

• Atom

  Pressing the button labeled Atoms will open up a small dialog box with a list of the atoms for the first item currently selected in the list of residues (an amino acid, heterogen, or water). One or more atoms can be selected from the list.

Atom Color Panel

The selection subpanel and radio buttons discussed further above can be used to apply a color change to a model, chain, region, amino acid, or atom. The Atom Color panel has three buttons for changing color on the current selection:

• Chooser

  Opens a color chooser box for selecting any color.

• Atom Type

  Colors the current selection by atom type using the CPK (Corey, Pauling, and Koltun) color scheme. The color scheme is documented in more detail in the CPKColorEnum and AtomEnum enumerations in the ProteinShader API.
  
  C: light gray
H: white
N: light blue
O: red
S: yellow


• Amino Acid

  Colors the current selection based on amino acid type. The colors listed below are documented in more detail (with RGB values) in the AAColorEnum enumeration in the ProteinShader API.
  
  Black: unknown amino acid
Blue: LYS and ARG
Bright red: ASP and GLU
Cyan: ASN and GLN
Dark gray: ALA
Green: LEU, VAL, and ILE
Light gray: GLY
Mid blue: PHE and TYR
Orange: SER and THR
Pale blue: HIS
Peach: PRO
Pink: TRP
Yellow: CYS and MET


Atom Visibility Panel

The Atom Visibility subpanel provides fine-grained control of visibility in an atom-style display (Space Filling, Balls and Sticks, or Sticks), whereas the Visibility menu above the canvas provides only a coarse level of control over whether amino acids, heterogens, or waters are allowed to be displayed. The selection subpanel and radio buttons discussed further above can be used to apply a visibility status change to a model, chain, region, amino acid, or atom. The Atom Visibility panel has three buttons and a slider for changing the visibility status on the current selection:

• Opaque

  Sets the current selection to visible and non-translucent.

• Invisible

  Sets the current selection to invisible.

• Translucent

  Sets the current selection to be semi-transparent. The percent translucency can be set from 0 to 100 by using the slider at the bottom of the panel, or by clicking the Translucent button after entering a number in the text box right below the button. A translucency of 99 % is nearly invisible, while 1 % is nearly opaque.

Atom Scale Panel

The selection subpanel and radio buttons discussed further above can be used to apply an atom scale change to a model, chain, region, amino acid, or atom. The scale changes apply to the radius of the spheres used in a Space Filling or Balls and Sticks style display.

The default radius for spheres in a Space Filling-style display is the Van Der Waals radius, while the default radius for spheres in a Balls and Sticks display is the covalent radius multiplied by a BALL_SCALE factor of 0.2. The Van Der Waals radius and covalent radius for each atom type are given in the AtomEnum enumeration of the ProteinShader API, where the BALL_SCALE factor is also specified.

Tiling Panel

Most graphics cards ultimately draw only points, lines, and flat polygons, so three-dimensional curved surfaces are approximated by drawing a large number of flat polygons that are tiled together to form a continuous surface, and lighting effects are used to help smooth out their appearance. The larger the number of polygons, the closer the image comes to a true curved surface, but the slower the scene will be rendered.

In an atom-style display, the ProteinShader program uses camera distance to calculate the level of detail that each sphere and cylinder is drawn at. When the camera is zoomed in to look at a small region of a protein, a high level of detail is used to provide better image quality. When the camera is zoomed out to look at the whole protein, a lower level of detail is used so that the image can be rotated more smoothly. This automatic calculation of the level of detail can be shut off by deselecting the Auto Tiling checkbox near the top of the Tiling panel. Once automatic tiling is shut off, the controls below the checkbox can be used to apply a fixed level of detail to spheres and cylinders.

As a way of expressing the level of detail that a sphere is drawn at, the concept of a tiling number is used. A tiling number of n means that if the sphere was drawn as a wireframe, the latitude lines would divide it into n stacks from pole to pole and the longitude lines would divide it into n slices around the equator. Therefore, the total number of flat panels that comprise the surface of the sphere would be n-squared. The concept of tiling number also applies to cylinders, except that the tiling number only refers to the number of slices about the equator because a cylinder does not curve along its length.

By using the radio buttons and menus of the Tiling panel, a fixed tiling number can be set for the spheres used in a Space Filling or a Balls and Sticks display. Similarly, a tiling number can be set for cylinders in a Balls and Sticks or Sticks display. Tiling number can also be set for the small spheres that are used as end caps for cylinders.