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View options

The full View Options menu contains a wide variety of settings.

The View Options menu in Foldit controls how the protein is displayed in the main window. The View Options menu can be accessed from the side menu on the left of the screen or using the default hotkey Alt+V.

The short View Presets panel is normally displayed first. View Presets allows selecting predefined groups of view options. Default presets are provided, and users can modify these presets or define their own.

View Presets panel

View presets

The shorter View Presets menu allow quickly changing multiple view options.

The View Presets panel is normally displayed first. On the View Presets panel, the "Select View Preset" list allows quickly selecting a set of view options. The "More View Options" button opens the full View Options panel. The "New" button creates a new view preset using the current view options. The "Edit" button allows changing an existing preset, and "Delete" deletes an existing preset.

View Options panel

The full View options menu allows adjusting all view options. The current settings on this panel can be saved as a new view preset. If a view preset was already open, it can be updated using the current settings.

The panel has several sections, covering different types of view options.

View Options section

In the View Options menu, the main View Options are shown in a column on the left, which continues across the bottom of the panel. See the View Options Gallery for examples of what the various option do. The options are:

  • Show clashes - default - displays spiky red balls when portions of the protein are too close to each other
  • Show exposed - default - displays yellow blobs when hydrophobic amino acids are on the outside of the protein
  • Show voids - default - displays translucent red spheres in empty areas on the inside of a protein
  • Show backbone issues - highlights backbone problems with a red exclamation point icon
  • Show bonds (sheet) - default - displays edgewise hydrogen bonds for segments marked as sheet
  • Show bonds (helix) - displays backbone hydrogen bonds for segments marked as helix
  • Show bonds (loop) - displays backbone hydrogen bonds for segments marked as loop
  • Show bonds (sidechain) - displays hydrogen bonds for sidechains - sidechains with bonds are displayed regardless of "View Sidechains" settings - also green-and-yellow "candy cane" shown for disulfide bridges
  • Show bonds (non-protein) - displays hydrogen bonds between protein and ligands or other non-protein molecules
  • Show bondable atoms - displays red and blue spheres to highlight atoms which can form hydrogen bonds - red spheres can bond to blue spheres
  • Show constraints - (default) - shows thin red lines to indicate presence of constraints used to hold parts of the protein in place
  • Show expected residue burials - shows a blue halo around hydrophobic amino acids that are expected to be buried or hidden in the inside of the protein
  • Show isosurface - displays the isosurface as a translucent cloud in shades of red and blue
  • Show Symmetric Chains - in a symmetry puzzle, displays the symmetric copies of the main chain
  • Symmetric Chain Colors - in a symmetry puzzle, uses a different color for each symmetric copy of the main chain
  • Color mutated segments - in a design puzzle, color any mutated segments in light blue, regardless of Color setting
  • X-ray tunnel for ligand - in a ligand puzzle, displays a black circle around the ligand, makes the portion of the protein within the circle invisible
  • Use relative color scoring - modifies Score coloring, reserves darkest reds for worst-scoring segments
  • Color relative to guide - for puzzles with a guide, adjusts coloring to show how close a segment is to corresponding segment in the guide
  • Show guide - for guide puzzles, display the translucent guide protein
  • Pulse guide - for guide puzzles, pulse the guide
  • Fade GUI - fades parts of the user interface while the protein is being moved
  • Hide GUI - hides parts of the user interface, such as the scoreboard and the chat/notification area
  • Show sidechains with clashes or exposeds - regardless of the View Sidechains options, shows sidechains for segments which contains exposed hydrophobics or which clash with other segments
  • Show outlines - for the Cartoon or Cartoon Thin options, include black lines to emphasize shape
  • Light background - display a light background in the main window
  • Pulse when working - pulsate the protein while operations like shake and wiggle are running
  • Orthographic - uses orthographic projection as opposed to the normal perspective view
  • Show grid - shows grid of 1-Angstrom squares

Color section

The Color section appears on the upper right of the full View Options panel, above the View Protein section. The Color options are:

View Protein section

The View Protein section appears on the right of the full view Options panel, below the Color section. See the View Protein Gallery for examples. The View Protein options are:

  • Cartoon - default - displays familiar visualizations of helixes and sheets
  • Cartoon Ligand - a Cartoon view tailored for puzzles with ligands
  • Cartoon Thin - slightly thinner version of Cartoon
  • Line - thin lines replace backbone and sidechain, no special visualization for helixes and sheets
  • Sphere - all non-hydrogen atoms are represented by colored spheres
  • Stick - similar to Line, but heavier tubes used, probably most useful with CPK or EnzDes color option
  • Trace Line - similar to Line, using slightly heavier lines
  • Trace Tube - uses a larger diameter tube than Cartoon, but no special treatment of helix and sheet, as in Line and Stick

View Sidechains section

The View Sidechains sections are shown on the right side of the full View Options panel, below the View Protein section. The View Sidechains options are:

  • View Sidechains/Don't Show (Fast) - sidechains are not displayed, minimizing the amount of drawing needed, and speeding up most operations
  • Show Stubs - the default option, shows a short stub instead of the complete sidechain - hovering over the stub displays the full sidechain
  • Show All (Slow) - - displays all sidechains, increasing the amount of drawing needed, and slowing down most operations

Miscellaneous controls

The buttons at the bottom of full Foldit user interface/View Options|View Options]] menu work with sets of view options.

  • Default view options - resets all view options to default values
  • Preset options - switches to the View presets panel
  • Save As - saves the current view options as a new view preset
  • Save - saves the current view options to the current preset, or creates a new preset

References

View options video by drumpeter18yrs9yrs

Foldit blog discussions of Show backbone issues option and the idealize tool

Background information on the colors used in the JMOL protein viewer: JMOL colors

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