NMRViewJ supports both automatic and manual peak picking. The automatic peak picker is simple and robust, identifying local maxima above the displayed contour threshold. A new noise thresholding tool can determine an estimate of the local noise value at each data point in the spectrum. In this mode the peak picker will ignore peaks in areas of high local noise, like stripes from the residual water, but find valid peaks immediately adjacent to the noisy region. Pseudo-3D spectra, for example a series of 2D HSQC spectra in one matrix, can be picked plane by plane. Manual picking can be done with the cursor in a mode that finds the local maxima or is restricted to the exact cursor location.
Interactive Peak Adjustment
With the cursor in "selection" mode the positions of peaks and the size of the peak footprint can be interactively adjusted. Peak labels, which can be the peak number, or other values such as the assignment or residue number, can be interactively moved. Multiple peaks can be selected (selected peaks have a transparent yellow color) and then deleted.
The Peak Inspector displays detailed information about each peak such as assignments, intensities, volumes and chemical shifts (and can be expanded to show more information). Peaks can be manually assigned by typing in values into the label field. If a molecular structure is present the display will indicate assignments inconsistent with the sequence. Here a peak is labelled as G46, but the residue at position 46 is an Ala, not Gly. As shown here, peaks have both a label, and an explicit assignment to an atom in the molecular structure.
While the Peak Inspector gives detailed information about an individual peak, the Peak Table summarizes information about all peaks in a given peak list. Like all tables in NMRView the peak table can be sorted based on the information in one or more columns. Here it is sorted by the chemical shift of dimension one. There is a default set of columns displayed for peak tables, but with simple commands you can alter it to display any of the peak attributes. Highlighted peaks can be marked for deletion. Sorting by intensity and then highlighting and marking a range of peaks is an easy way to remove weak peaks.
The Peak Identification tool can be used to suggest assignments for any peak. Each peak list has attributes that describe the type of peaks expected (a pattern specifying the types of atoms and inter-dimensional relations specifying which dimensions specify chemically bonded atoms) and tolerances. The Peak Identifier finds atom assignments whose atom types and chemical shifts are consistent with the peak's position and the list's attributes. If a molecular structure (or family of structures) with coordinates is present then the Peak Identification table will provide information not only about the chemical shift alignment with the atoms, but also the interatomic distances in the structures.
Each dimension of each peak is linked to an internal NMRViewJ object known as a Resonance. Peaks that represent the same atom can be linked to a single resonance. Assignment of the peak label, actually assigns a label to the resonance, so that all linked peak dimensions are simultaneously assigned. NMRViewJ tools such as RunAbout make extensive use of the Resonance concept. Illustrated here is the Resonance Table that lists all the resonances present in the current project. The displayed chemical shift in the table is the average of all the shifts of the peak dimensions connected to that resonance. Double clicking on a table row allows you to "drill down" into the constituent peaks. Since peak lists can have a condition associated with them it is possible to use the Resonance table to get the average chemical shift for each resonance collected under a specific condition.
Peak Atom Matching
Sometimes one has an unassigned peak list, but a set of chemical shift assignments for a protein. Perhaps, you used NMRViewJ to read in the assignment table of a BMRB STAR file and now want to use those assignments to assign the peaks. The Peak Atom matcher is the tool for you. It calculates an optimal assignment between the set of peaks and the set of atom assignments. Resonances, see above, can be linked not only to peak dimensions but to specific atoms. After calculating and displaying the optimal assignment, you can link aligned peaks with their atoms, thereby transferring the chemical shift assignment to the peak.
Peak Peak Matcher
The Peak Peak matcher works with the same underlying algorithm (a maximally weighted bipartite graph algorithm) to find the optimal matching of peaks in one list with peaks in another list. This can be useful, for example when matching up sets of peaks collected in aligned and unaligned media. The peak peak matcher can optimize the global offset in each dimension between the two peak lists. Again, when it's done, you can link peaks so that matched peaks share the same resonance. If one peak is assigned and one not, this will effectively transfer the assignments from the assigned list to the unassigned list.
The Peak Coupler finds peaks within a list that differ by a certain tolerance in each dimension and replaces them with a single peak at the average position. Typically one will use a tolerance larger than the expected coupling in one dimension, and smaller values corresponding to the random peak deviation in the other dimensions. This is often useful on NOE lists that are at high enough resolution to have a splitting from the amide - alpha coupling. Collapsing the coupled peaks to a single peak makes the assignment and quantification easier. The auto mode will do several rounds of coupling in each dimension as a way to collapse peaks in homonuclear COSY spectra.
Peak Reading and Writing
The primary way to store store peak data in an ongoing NMRViewJ project is to use the STAR files. But if you want to import and export peak files to exchange information with other NMR analysis programs you can read and write in a variety of formats. Besides the NMRView peak list format it will read in files from SPARKY and generate XML format files for use with ARIA.
Peak Intensity Plotting
NMRViewJ can display with graphical charts any information you can extract from your data. There are built-in commands available in the Peak menu to allow you generate plots of peak intensities and volumes. These can be useful for getting an overall view of the thresholds used in peak picking.
Heteronuclear NOE analysis
NMR has a wide variety of possible experiments and each one can involve some sort of custom data analysis. NMRViewJ has built-in tools for various analysis routines. Illustrated here is the tool for analyzing heteronuclear NOE experiments. The tool takes peak positions from one peak list and then measures the peak intensity, in a variety of possible ways, in the datasets measured with and without the NOE effect active. Intensity ratios and errors are presented in a table that can be exported to a text file. This tool makes use of some simple scripts that combine analysis with a graphical user interface. You can create your own tools.
IPAP tool for dipolar couplings
This is another experiment specific tool that can be used to determine residual dipolar couplings and export the calculated values into tables in several formats.
Peak and Atom Residue Shifter
Did you do all your assignments with residue numbering starting at "1", and now realize you wish you had them all starting at "173". This shifter will adjust all atom and peak assignments by a specified residue offset.