This visualization shows a schematic structure of the relevant molecule, in combination with the ambiguity 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 ambiguity code value or atom type, as follows:
Index value | Definition | Color |
---|---|---|
Unknown | White | |
1 | Unique | Dark brown |
2 | Ambiguity of geminal atoms or geminal methyl proton groups | Light brown |
3 | Aromatic atoms on opposite sides of the ring (e.g. Tyr HE1 and HE2 protons) | Light blue |
4 | Intraresidue ambiguities (e.g. Lys HG and HD protons) | Purple |
5 | Interresidue ambiguities (Lys 12 vs. Lys 27) | Magenta |
9 | Ambiguous, specific ambiguity not defined | Yellow |
Element | Color |
---|---|
Carbon | Gray |
Hydrogen | White |
Oxygen | Red |
Nitrogen | Blue |
Sulfur | Orange |
Phosphorus | Pink |
The default is to have the atoms colored by ambiguity code value, but this can be changed to coloring by atom type by dragging the cursor in the color select view.
Note that H, HA, HA2, and HA3 atoms are treated as part of the backbone in this visualization.
The ambiguity code legend shows the colors for the various ambiguity codes (or the colors for the elements, if coloring by atom type is selected).
The data view shows the fraction of atoms in each residue having the selected ambiguity code, relative to the total number of C, H, and N atoms in the appropriate amino acid. For example, if five atoms have the selected ambiguity code in a residue that is a histidine, the value displayed in the graph for that residue will be 0.294. The cursor in this view selects residues according to the data values -- residues for which the red tip of the bar are enclosed in the cursor are selected.
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 ambiguity codes. 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.
The info view shows the BMRB accession number and generation date of the visualization; show the view help (F1 key) to see the Peptide-CGI version and exact generation timestamp.