Atom Assignment Table

The chemical shift values for assigned atoms are displayed in the Atom Assignment Table. This table shows one row for each atom in your molecular structure. It's easy to limit the displayed atoms to a certain set ("*.C,N,CA for backbone atoms, 23.H* for the protons of residue 23, etc.). Not only is the assigned shift shown, but it also shows a reference chemical shift calculated in one of several ways. Built-in options include average values from the BMRB and random-coil values calculated with NMRViewJ. You can also import assigned chemical shifts from STAR files so you can compare your values with those from another assignment of that protein. The assigned shift, the reference shift, and various calculations (scaled by standard deviation from reference data, for example) of the deviation are shown. Like all NMRViewJ tables, it's sortable, so you could for example sort by deviation from standard values to look for outliers.

Reading and Writing Chemical Shifts

As with peak lists, you can import and export chemical shift assignments. For example, you can export in the format used by NMRViewJ, BMRB STAR2 and STAR3, ARIA (including the XML format), TALOS, and CYANA.

CSI Plots

Assigned chemical shifts can be displayed as CSI plots. Thanks to contributions from our users there are a variety of reference shifts that can be used, including those relevant to unfolded proteins.

LACS Plots

A relatively recent way of plotting protein chemical shifts is with the Linear Analysis of Chemical Shifts. NMRViewJ can generate this plot for CA, CB, HA, and C atoms. The fitted lines should intersect at 0,0 if your data is properly referenced so this is a good way to check your referencing, and to look for outliers.

Minimum Chemical Shift

One way to assess the effect of ligand binding without needing to assign the ligand bound state as well as the free state is with the Minimum Chemical Shift method. NMRViewJ has a tool for this that will give you a table indicating a lower limit on the amount each residue's peak has shifted.

News

2 August 2016: New Versions of NMRView, dataChord Spectrum Miner and Analyst, and NvFX

New Google Groups for NMRViewJ and NMRFx Processor

Our first publication on NMRFx appears at the Journal of Biomolecular NMR