Analyse structures

Instructions

To analyse structures in Analysis, open the Structure: Structures popup using M: Structure: Structures. In the {Ensembles} tab, you now see the structure ensembles. To view the structures select an ensemble and click [Viewer]. This raises the Structure: Structure Viewer popup (structure viewer, shown below) where structures in the ensemble can be selected for display in the “Model” pulldown menu. The controls for the structure viewer are as follows:

• • Rotate with the arrow keys or middle mouse and drag.

  • Zoom with the mouse wheel.

  • Move with middle mouse + ‘Ctrl’  and drag.

  • The mouse right-click brings up a menu that allows you to change the display mode, spin, and print the structure.

  • The mouse left-click is used for atom selection.

Try the atom selection by first ensuring that the correct peak list is selected at the top, click on an atom and then click [Show Peaks]. This will raise Peak: Selected Peaks, which contains all the peaks that involve the atom selected in the structure. The numbers on the dashed lines in the structure viewer represent distances between the atoms. Take a look at a NOESY peak in a spectrum window and use the Assignment: Assignment Panel popup for inspection. Distances between the atoms indicated by dashed lines can be shown by clicking the [Show On Structure] button.

Select an ensemble in {Ensembles} and go to {Structure Models}. Click [Calculate RMSDs] to see how well the structure models align.

The residues are listed in {Residues}, with information on backbone RMSD, all atom RMSD, Phi and Psi angles, and Ramachandran region. Select a residue and click [View Residue] to view the residue in the structure.

The atom coordinates are found in {Coords}.