This visualization shows the 3D structure of the relevant molecule, in combination with all of the other data 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 the 3D structure (rendered by Jmol). Note that you can control many options in the structure view with the popup menus in that view and the Jmol menu in the JavaScreen menu bar.
The residues and atoms selected in the atom select tree are highlighted in green. You have the option of highlighting the atoms with a "selection halo" or by coloring the atoms themselves (Jmol->View->Highlight in the menu bar). Atoms not colored for highlighting are colored as follows:
| Element | Color |
|---|---|
| Carbon | Gray |
| Hydrogen | White |
| Oxygen | Red |
| Nitrogen | Blue |
| Sulfur | Orange |
| Phosphorus | Pink |
The atom color legend shows the colors for the elements.
The data view shows one of the data sets available for this entry (selected by the data select view). The cursor in this view selects residues according to the data values -- residues for which the red tip of the bar is enclosed in the cursor are selected. By default, residues selected in this view are selected in the atom select tree.
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. All available data sets for the current entry are listed in this view; by dragging the cursor you select which data set is shown in the data view.
The info view shows the BMRB accession number (and PDB ID, if relevant) and generation date of the visualization; show the view help (F1 key) to see the Peptide-CGI version and exact generation timestamp.
Selection of which atoms to display and highlight is now done in a separate window, to allow more space in the main window to be used for the structure view and data view.
The structure type tree selects which atoms are shown in the structure view by structure type (backbone, backbone and side chains, or backbone, side chains, and hydrogens). Changing what's selected in this tree also changes what is displayed in the atom display tree and the atom select tree.
The atom display tree selects which atoms are displayed in the structure view. The atom display tree allows selection of the entire molecule, or parts of the molecule by residue and individual atom. Changing what's selected in this tree also changes what is displayed in the atom select tree.
The atom select tree selects which atoms are highlighted in the structure view. The atom select tree allows selection of the entire molecule, or parts of the molecule by residue and individual atom. By default, the residues selected in the data view are also selected in the atom select tree. You can change which residues and atoms are selected by manipulating the tree. The Reset button sets the selection in the tree back to the residues selected in the data view.
Left-clicking the Jmol button in the JavaScreen menu bar brings up this menu.
Right-clicking in the structure (Jmol) view brings up this menu.
