The structure viewer popup is used to give 3D graphical representations of any structure in the Analysis project. The user can change the view of the displayed structure by rotating, zooming in and out and moving the structure around in the viwer. In addition to viewing structures, connections associated with peaks, constraints and NOE assignment can displayed when the structure viewer is working in conjunction with other popups, such as the Assignment: Link NOEs popup. Selections or changes made in other popups will change the structure views where appropriate. Parameters such as the residue RMSDs can be used to change the structure view using colour codes and atom sizes.

Using the right mouse button, the Structure viewer menu is accessible, which allows the user to reset the view, highlight the backbone, slowly rotate a structure and print a structure view to a file.

General controls

The Structure: Structure Viewer popup.

MolSystem: Structure

Specifies the structure in the project from which models can be displayed.

Model

Specifies the model in the ensemble to display.

Dist Method

Specifies the method used for calculating and showing distances between atoms. Options are:

• • NOE Sum

  • Min Dist

The NOE Sum option displays a r^-6 sum average over the selected atoms, e.g in the case of a methyl group. The Min Dist option shows the minimum distance between the selected atoms or atom groups.

structFrame

The frame containing the structure view.

Reset

Resets the view of the structure. All labels are removed and the view is set back to a plain stick view.

RMSDs

This option applies a colour code and adapts the sizes of atoms for the residues based on the RMSD. The colours and sizes of atoms depend on the RMSD, which are per residue RMSDs calculated in an ensemble. Small atoms and blue colour correspond to small values of the parameter; Large atoms and yellow colours correspond to larger values of the parameter. See also Structure: Structure Ensembles, [Display Params].

Display Params

This option applies a colour code and adapts the sizes of atoms for the residues in the popup. The colours and sizes of atoms depend on the value of the parameter selected under the 'Structure Parameter' pulldown, which are per residue RMSDs calculated in an ensemble. Small atoms and blue colour correspond to small values of the parameter; Large atoms and yellow colours correspond to larger values of the parameter. See also Structure: Structure Ensembles, [Display Params].

Structure Parameter

Specifies the parameter that is used for the [Display Params:] button. Options are:

• • RMSD: CA

  • RMSD: CB

  • RMSD: H

  • RMSD: O

  • RMSD: All

  • RMSD: Backbone