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The View Options menu in Foldit controls how the protein is displayed in the main window. The View Options menu is accessed differently depending on which version of the Foldit user interface is selected.
ViewOptions.advanced.defaults

View Options menu with "Show advanced GUI" selected in General Options.

Accessing View Options Edit

In the original interface, the View Options menu is available through the View dropdown on the lower menu bar.

In the selection interface, the View Options menu is available through the View Options icon in the vertical menu. Click on the Foldit icon in the lower left-hand corner to display the vertical menu. The View Options menu is also available through the "v" keyboard shortcut.

Advanced GUI Edit

There are two versions of the View Options menu, depending on whether the "Show advanced GUI" is selected in General Options menu. The General Options menu is available via the ctrl+t (hold control key, type lowercase "t") in both the original and selection interfaces. In the original interface, General Options is a selection on under Menu. In the Selection Interface, click on the Main icon or use the "p" keyboard shortcut to display the main menu.
GeneralOptions.ShowAdvancedGUI

General Options menu with "Show advanced GUI" option highlighted.

Basic View Options Edit

Without the "Show advanced GUI" option, the View Options menu has two major sections and two additional options. There's also a "Default view options" icon, which can reset the options to their initial settings.

View Options section Edit

In the View Options menu, the main View Options are shown in a column on the left. 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 exposeds - 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 bonds - shows blue-and-white "candy canes" representing hydrogen bonds, and green-and-yellow candy canes for disulfide bridges
  • 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 - 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
    ViewOptions.basic.defaults

    Basic View Options when "Show advanced GUI" not selected.

View Sidechains section Edit

The View Sidechains options are shown on the right side of the View Options menu. These options are the same regardless of whether the "Show advanced GUI" is selected.

The options are:

  • 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

Additional options Edit

There are two additional options shown in the lower right of the View options menu.

  • Show sidechains with clashes or exposeds - regardless of the View Sidechains options,

shows sidechains for segments which contains exposed hyrdophobics or which clash with other segments

  • Show guide - some puzzles have a translucent guide, this option displays the guide when present

Advanced View Options Edit

With the "Show advanced GUI" option selected, the View Options menu contains many more settings. There are new "Color" and "View Protein" sections. The "View Options" section is expanded, and there are several new additional options.

View Options section Edit

In the View Options menu, the main View Options are shown in a column on the left. The advanced View Options include additional settings for displaying hydrogen bonds, and options to highlight backbone issues and show the isosurface of the protein. 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 exposeds - 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 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

Color section Edit

In the advanced View Options menu, the Color section appears on the upper right. The Color options are:

  • AAColor - displays a unique color for each amino acid
  • AbegoColor - colors the segment according to the nearest Rama Map region
  • CPK - colors sidechain atoms based on CPK coloring
  • EnzDes - EnzDes is very similar to CPK
  • Hydro - displays hydrophobic amino acids in orange, hydrophilic amino acids in blue
  • Hydro/Score - backbone is colored as in Hydro, sidechains or stubs as in Score
  • Hydro/Score+CPK - as in Hydro/Score, with sidechains as in CPK
  • Rainbow - color changes based on segment number, first segment is violet, last segment is red
  • Score - poorly scoring segments are shown in red, better scoring segments in green
  • Score/Hydro - backbone colored as in Score, sidechains and stubs as in Hydro
  • Score/Hydro+CPK - as in Score/Hydro, with CPK coloring added to sidechains

View Protein section Edit

In the advanced View Options, the View Protein section on the right offers several new visualizations that affect the entire protein. See the View Protein Gallery for examples. The options are:

  • Cartoon - default - displays familiar visualizations of helixes and sheets
  • Cartoon Thin - slightly thinner version of Cartoon
  • Line - thin lines replace backbone and sidechain, no special visualization for helixes and sheets
  • Line+H - same as Line, except hydrogen atoms are visible
  • Line+polarH - same as Line+H, but only polar hydrogens, which may contribute to electron bonds, are shown
  • 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
  • Stick+H - same as Stick, but hydrogen atoms are shown as Line+H, and appear in white with CPK or EnzDes color
  • Stick+polarH - same as Stick+H, but only bondable hydrogens shown as in Line+polarH
  • 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 Edit

The View Sidechains options are shown on the right side of the View Options menu. These options are the same regardless of whether the "Show advanced GUI" is selected.

The options are:

  • 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

Additional options Edit

When "Show advanced GUI" is selected, there are several additional options that affect how the protein is displayed.

  • 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 hyrdophobics or which clash with other segments

  • Show outlines - for the Cartoon or Cartoon Thin options, include black lines to emphasize shape
  • Dark background - display a dark background in the main window
  • Pulse when working - pulsate the protein while operations like shake and wiggle are running

References Edit

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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