Importing Structure Calculation Results

Loading a pre-prepared project

You can see the CCPN project that resulted from this completed ARIA run by loading the project CcpnStructCourseD: In the menu bar select M: Project: Open Project then [Yes] to close the current project and [No] to not save. Navigate to find and select the CcpnStructCourseD project, then click [Open]. This project will be used in the rest of this tutorial. Although we are using a pre-prepared CCPN project, to use the CCPN project that was generated by ARIA on the CCPN Grid it simply has to be downloaded. We will now have a look at the result of the structure calculation by using Analysis.

Structures

In the data that comes back from ARIA we will see that two structure ensembles have been entered into the CCPN project; one from the last ARIA iteration and one after the water refinement stage. To see the structures go to M: Structure: Structures. If you go to the {Structure Models} tab select the [Superpose & Calculate RMSDs] button at the top right and then [OK] to see how well the structural models align. To see the structure in a 3-dimensional representation for whichever is selected in the table click the [Viewer] at the top:

The controls for the structural viewer are as follows:

• • Rotate with middle-click & drag.

  • Zoom with the mouse wheel, or middle-click, 'Shift' & drag.

  • Move with middle-click, 'Ctrl' & drag.

The mouse right-click brings up a menu that allows you to change the display mode, spin, and print the structure. The left-click is used for atom selection. Try the atom selection by first ensuring that the N-NOESY peak list is selected at the top, click on an amide location on the structure (i.e. a blue atom) and then click [Show Peaks]. This will show a table containing all of the peaks that relate to connections from the selected atom in the structure. The numbers on the dashed lines represent the distances between the atoms.

The same sort of functionality is present in the Assignment: Assignment Panel popup (M: Assignment: Assignment Panel). If you look at the NOESY spectrum in window2, and assign a peak (by pressing 'a' with the cursor over a peak), you can see assignment possibilities via the [Show On Structure] button. Also note that because we now have a structure the Assignment: Assignment Panel popup will show distances between one peak assigned 1H resonance and the 1H possibilities in another peak dimension:

Referring back to the restraints popup (M: Structure: Restraints & Violations, {Restraints}), set the structure pulldown menu to "2"; the structure from the ARIA/CNS water refinement. Next set the restraint list as one of the Distance lists. You will see that the "Struc Value" is now filled-in for the restraints and you are are able to select any restraint rows (using 'Shift'/'Ctrl' keys) and then click [Show Selected On Structure] to illustrate graphically where on the loaded structure the restraints apply.

Previous: Submitting a Structure Calculation to CCPN Grid

Next: Restraints and Violations