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.
To move and rotate the three-dimensional coordinate display the following
keyboard controls may be used:
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
MolSystem: Selects which molecular system to select a structure for
Ensemble: Selects which structure ensemble to display, for the specified molecular system
Model: Selects which conformational model of the selected structure/ensemble to display
Peak List: When using the “Show Peak” option, sets which peak list is used to display atom connectivities
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
Reset: Remove all highlights and connections from the structure display
RMSDs: For an ensemble, calculate the per-atom coordinate root mean square deviations and adjust atom size and colours accordingly
Display Params: Display the selected structural parameters on the structure, adjusting atom labels, size and colours accordingly
*None*: Selects which structural parameters, from those calculated, to display on the structure
Show Peaks: In the stated peak list, display peak assignment connectivities between the highlighted atoms (left click to select atoms in the display)
Clone: Clone popup window
Help: Show popup help document
Close: Close popup