The Idealize tool adjusts the lengths and angles of peptide bonds in the protein backbone. The lengths and angles, also known as "degrees of freedom", can vary, but only within a narrow range. The idealize tool sets the angles and lengths to "ideal" values based on theoretical calculations. The measurements of real proteins are very close to these ideal values.
See the blog post The Idealize Tool for background on the idealize tool. The diagram shown here was originally referenced in the blog post.
As with other tools in Foldit, the exact details of how idealize works are not known. Foldit does not offer direct measurements of the angles and lengths shown in the diagram.
In the original interface, the idealize tool is available by hovering over a segment, right-clicking (or shift-clicking), and selecting "Idealize" from the wheel menu.
The original interface version of the idealize tool adjusts the peptide bonds of multiple segments, based on secondary structure. When hovering over a sheet or helix section, the tool updates all segments in the sheet or helix, and any adjoining loop segments.
When hovering over a loop segment, the original interface idealize tool adjusts not only the loop, but adjoining sheet or helix sections, and any loop sections adjoining the sheets and helixes. This means a large number of segments can be affected one idealize action.
The "Show Backbone Issues" setting in View Options highlights spots where the peptide bonds are especially bad. Clicking on the exclamation point (bang) icon idealizes just one peptide bond. This allows finer control over what gets idealized in the original interface. The drawback is that only the worst peptide bonds can be idealized this way.
In the selection interface, the "Idealize Peptide Bonds" tool (shortcut key 2) is available when two or more adjacent segments are selected. The tool is also available when there are multiple non-adjacent areas selected, but each area must have two or more segments selected. This selection interface version of the idealize tool allows much more control over what is idealized.
In a recipe, the function structure.IdealizeSelected is the equivalent to using "Idealize Peptide Bonds" tool manually. The function idealizes peptide bonds of any sections of two or more selected segments.
Bond angles and lengths[edit | edit source]
The diagram shows bond angles and lengths for a peptide bond. The peptide bond involves the C (carbon) and N (nitrogen) atoms in the center of the diagram.
The bonds between atoms are shown as straight lines.
Bond lengths are shown in angstroms, indicated by Å in the diagram.
Bond angles are shown in degrees. Bond angles are shown for only two atoms, the carbon and the nitrogen of the peptide bond.
See protein backbone for further discussion
This version of the diagram was retrieved from http://curser.science.ru.nl/content-e/pub_NWI/Bioinformatics%20Summerschool%202006%20light%2003092006/documents/do_6546.htm
The original post The Idealize Tool included the same diagram, hosted on the Rockefeller University website (rockefeller.edu). The same diagram appears in several other spots on the internet. At one point, the diagram was unavailable from rockefeller.edu, but it has since reappeared.