S2 Predicted vs. Experimental Values

This visualization shows the 3D structure of the relevant molecule, in combination with the predicted and experimental S2 order parameter values. (Predicted values are determined from the relevant PDB structure by s2predict.)

Main Visualization Window

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 (see below) 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:

Atom type colors
Element Color
Carbon Gray
Hydrogen White
Oxygen Red
Nitrogen Blue
Sulfur Yellow
Phosphorus Orange

The data view shows the predicted and experimental S2 order parameter values for each residue. The DEVise cursor in this view selects a residue to highlight. By default, residues selected in this view are selected in the atom select tree (see below).

The data scroll view scrolls the X axis of the data view. The DEVise 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 primary structure view shows the single-letter abbreviation for the amino acid for each residue in the molecule.

The secondary structure view shows a color code for the secondary structure of the molecule at each residue.

The secondary structure legend shows a legend for the colors in the secondary structure view.

The info view shows the BMRB accession number and PDB ID and the generation date of the visualization; show the view help (F1 key) to see the Peptide-CGI version and exact generation timestamp.

Structure Selection Window

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.

JavaScreen Menubar Jmol Menu

Left-clicking the Jmol button in the JavaScreen menu bar brings up this menu.

Jmol Popup Menu

Right-clicking in the structure (Jmol) view brings up this menu.

Jmol Mouse Functions