Assignment Figure of Merit Visualization

This visualization shows a schematic structure of the relevant molecule, in combination with the assignment figure of merit values available for this entry.

The visualization is laid out as shown below; the view names are referred to in the text.

The structure (main) view shows a schematic structure. The sections of the structure belonging to residues selected in the data view are highlighted in green. All other atoms are colored by either figure of merit value or atom type, as follows:

Figure of merit value colors
Value Color
Unknown White
>=99% Dark brown
>=96% (and < 99%) Light brown
>=90% (and < 96%) Light blue
>=70% (and < 90%) Purple
>=50% (and < 70%) Magenta
>=10% (and < 50%) Yellow
<10% Red
Atom type colors
Element Color
Carbon Gray
Hydrogen White
Oxygen Red
Nitrogen Blue
Sulfur Orange
Phosphorus Pink

The default is to have the atoms colored by figure of merit value, but this can be changed to coloring by atom type by dragging the cursor in the color select view.

The figure of merit legend view shows the colors for the various figure of merit values (or the colors for the elements, if coloring by atom type is selected).

The data view shows the fraction of atoms of the selected type (backbone, side chain, H) in each residue having figure of merit values within the selected range, relative to the total number of the selected type of atoms in the appropriate amino acid.

Note that, for a given residue, the fraction of atoms with a figure of merit >= 95% and the fraction with a figure of merit < 95% may not add up to 1.0, since the denominator of the fraction is the number of atoms expected in the given amino acid, not the number for which we have figure of merit values.

The data scroll view scrolls the X axis of the data view. The cursor selects the range of residues shown in the data view -- you can drag the entire cursor, or drag the left or right edge to change its size.

The data select view selects which data set is shown in the data view; in this case, the data sets are the the different combinations of structure (backbone, side chain, or hydrogen) and figure of merit >= 95% or < 95%. All available data sets for the current entry are shown in this view; by dragging the cursor you select which data set is shown.

The atom select view selects which atoms are shown the structure view (backbone, backbone and side chains, or backbone, side chains, and hydrogens). The default is backbone and side chains.

The residue list view lists the residue number and amino acid for each residue. Residues selected in the data view are highlighted in green in this view. The cursor (which is linked to the cursor in the residue select view) selects which residues are shown in the structure view.

The residue list scroll view scrolls the residue list view. The cursor can be dragged to select the range of residues shown (note that this cursor is fixed-size).

The residue select view selects which residues are shown in the structure view -- all residues within the cursor are shown. This cursor is a variable-size cursor. The default is to show all residues.


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