Distance Restraints

This visualization shows the 3D structure of the relevant molecule, in combination with distance restraints.

Sections of this document:


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. For distance restraints, the 3D display defaults to wireframe mode, but you can change it to other modes using the Jmol menus. Restraints are drawn in this view according to the selections in the entity assembly select view, the violation select view, the ambiguity select view, the restraint length select view and the data view.

Note that for restraints with pseudoatoms, a line is drawn for each possible "real" atom at each end of the restraint.

Restraints are colored as follows:

Restraint colors
Type Color
Non-violated, non-ambiguous Yellow
Violated, non-ambiguous Orange
Non-violated, ambiguous Cyan
Violated, ambiguous Magenta

Any atoms selected in the 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 or bonds themselves (Jmol->View->Highlight in the menu bar). Atoms or bonds 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 atom color legend shows the colors for the elements.

The data view shows the number of restraints per residue, given the selection in the entity assembly select view, the violation select view, the ambiguity select view, and the restraint length select view. The DEVise cursor in this view selects residues according to the data values -- a residue for which the red tip of the bar is enclosed in the cursor is selected.

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 entity assembly select view selects the entity assembly for which data is shown in the data view. If the entry being visualized has only one entity assembly, this view has no effect.

The violation select view selects the violation state for which data is shown in the data view. If this entry has no data on violations, only the option "all" is shown.

The ambiguity select view selects the ambiguity state for which data is shown in the data view. If this entry has no data on ambiguities, only the option "all" is shown.

The restraint length select view selects the length of restraint for which data is shown in the data 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.

Main Visualization Window (structure closeup)

This image shows both the structure view and the data view zoomed in to show a finer level of detail. Note that the cursor in the data view is forced to be entirely within the view, so zooming in may shrink the cursor.

Structure Selection Window

Selection of which atoms to display and highlight is 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. Note that if, for example, you elect not to display side chain protons, then no restraints involving side chain protons will be displayed.

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. Note that if an atom is not displayed, any restraints involving that atom are not displayed.

The atom select tree enables you to select entities, residues, and atoms to be highlighted in the 3D view. The atom select tree allows selection of the entire molecule, or parts of the molecule by residue and individual atom. The Reset button sets the selection in the tree back to the atoms 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