Structure : Structure Viewer

A Simple Graphical Display for Macromolecule 3D Coordinates

CcpNmr Analysis contains a simple 3D structure viewing module which is used to display NMR derived information on macromolecular coordinates. For example this viewer can be used to display alternative possibilities for NOE assignments as dashed lines that connect different parts of a molecular structure. The structural model may be moved and rotated by various means listed below. Also, specific atoms may be selected and de-selected in the display by left clicking.

The structures that may be displayed with this system are loaded in to the CCPN project via the main Structures popup window. A structure is chosen for display by selecting from the “MolSystem”, “Ensemble” and “Model” pulldown menus, i.e. at present only one conformational model is displayed at a time.

The “Peak List” selection is used in combination with the [Show Peaks] button at the bottom, which brings up a table listing all of the peaks, within the selected peak list, that relate to that atoms chosen (left mouse click) in the structural view.

Much of the NMR-derived information that is presented in the graphical display will be controlled via separate popups, for example the [Show On Structure] button of the Assignment Panel or [Show Selected On Structure] in the Restraints and Violations popup. Nonetheless, some data can be added to the display via the viewer directly; ensemble RMSDs and other validation parameters can be superimposed as coloured spheres of various sizes.

View Controls

To move and rotate the three-dimensional coordinate display the following keyboard controls may be used:

  • Rotate: Arrow keys
  • Zoom: Page Up & Page Down keys
  • Translate: Arrow keys + Control key

Or alternatively the following mouse controls:

  • Rotate: Middle button click & drag
  • Zoom: Mouse wheel or middle button click + Shift key & drag up/down
  • Translate: Middle button click & drag + Control key

Also an options menu appears when the right mouse button is clicked and the left mouse button is used to select and de-select atoms in the current model view.

Main Panel

pulldown MolSystem: Selects which molecular system to select a structure for

pulldown Ensemble: Selects which structure ensemble to display, for the specified molecular system

pulldown Model: Selects which conformational model of the selected structure/ensemble to display

pulldown Peak List: When using the “Show Peak” option, sets which peak list is used to display atom connectivities

pulldown Dist Method: Where the distances between sets of atoms are displayed, sets whether to use the NOE equivalent (sum r^-6 intensities) or minimum distance

button Reset: Remove all highlights and connections from the structure display

button RMSDs: For an ensemble, calculate the per-atom coordinate root mean square deviations and adjust atom size and colours accordingly

button Display Params: Display the selected structural parameters on the structure, adjusting atom labels, size and colours accordingly

pulldown *None*: Selects which structural parameters, from those calculated, to display on the structure

button Show Peaks: In the stated peak list, display peak assignment connectivities between the highlighted atoms (left click to select atoms in the display)

button Clone: Clone popup window

button Help: Show popup help document

button Close: Close popup

Table Of Contents

Previous topic

Structure : Structures

Next topic

Structure : Make Distance Restraints

This Page