Assignment

The Assignment menu provides access to all the functionality that is commonly used to assign resonances to specific atoms and residues. The menu is subdivided into 3 sections. The first section provides basic assignment functionality, consisting of the assignment panel, copying of assignments and quality reports. The second provides a streamlined procedure to connect HSQC root peaks to 3D spectra, pick 3D peaks and link sequential spin systems. The last section provides access to automated sequential backbone assignments of proteins.

Assignment Panel

Opens the Assignment: Assignment Panel popup. This popup provides the primary means to make peak assignments, and works together with the Molecules: Atom Browser popup. It displays the possible assignment options and the assignment status for a selected peak. The information in the assignment panel is displayed for the peak that was last selected and updated every time another peak is selected.

Copy Assignments

Opens the popup Assignment: Copy Assignments. This popup allows to copy assignments between selected peak lists, and even between molecule chains, if multiple chains are present.

Quality Reports

Opens the Assignment: Quality Reports popup. This popup provides statistics and quality reports on the atom assignment status, through space connectivities, resonances and peaks. Errors or suspicious assignments are highlighted, making it easy for the user to inspect possible problems or abnormalities.

Initialise Roots

Opens the Assignment: Initialise Roots popup. This popup allows to initialise root spin systems from a 15N-HSQC or HNCO spectrum that has been peak picked, and includes functionality to easily distinguish pairs of peaks originating from amide NH2 groups from backbone NH atom groups. The NH roots can be used for example as a basis to selectively pick peaks in NH-based 3D experiments that are commonly used for sequential backbone assignments.

Link Peak Lists

Opens the Assignment: Link Peak Lists popup. In this popup, the roots that have been initialised using Assignment: Initialise Roots can be used to navigate in selected windows and to perform fast selective peak picking and assignment of 3D peaks that occur at the root frequencies. The popup provides efficient automation options for a normally time consuming procedure, whilst at the same time limiting the picking of unwanted noise peaks and allowing manual inspection and intervention.

Link Sequential Spin Systems

Opens the Assignment: Link Sequential Spin Systems popup. This popup uses information from experiments that can be combined to identify sequential backbone connectivities in proteins. Peaks in these spectra, e.g. HNCACB and CBCAcoNH, are matched, and the popup displays the best matches and allows the setting of sequential connectivities. In addition, spin systems are automatically scored for residue types, and stretches of linked spin systems can be assigned directly to specific regions in the protein sequence using the residue type matches.

Link NOEs

Opens the Assignment: Link NOEs popup. This popup allows the user to refine NOE peak assignments based on chemical shift matches and inter atomic distances in (intermediate) structures in the project. The assignment possibilities are displayed in the structure viewer and the spectrum windows, which provides the user a complete overview of all the relevant information for making a NOESY assignment. NOESY peak assignments to individual or multiple assignments can be made directly from the panel.

Automated Backbone Sequence

Opens the Assignment: Automated Backbone Sequence popup. In this popup the user can setup the parameters and data and do an automated sequential backbone assignment with the program Nexus. Nexus results are displayed and can be analyzed and committed as correct assignments after validation by the user.