TABLE 2.
Sample input file names, description and data format.
| File name | Description | Format of data columns |
|---|---|---|
| dest.txt | DEST data | Residue number, Frequency of resonance in DEST dimension (15N for 15N-DEST) measured from 0 p.p.m. (Hz), Peak intensities as a function of frequency (N data points where N is the number of experiments including reference experiments) |
| frequencies.txt | Saturation offset of DEST saturation pulse | Offset from carrier frequency (Hz) for each data point in dest.txt in the same order, including a value of 0 for reference experiments |
| satfields.txt | DEST saturation field intensity as a function of offset | Saturation field (Hz) for each data point in dest.txt in the same order, with 0 used to specify reference experiments |
| R2.txt | Transverse relaxation rate in the NMR-visible state | Residue number, R2 (s−1) |
| R1.txt | Longitudinal relaxation rate in the NMR-visible state (Note: as these values do not affect the result within the entire range of R1 for biomolecules, estimated values can be used) | Residue number, R1 (s−1) |
| deltaR2.txt | Difference in R2 between dark state and reference sample | Residue number, ΔR2 (s−1), s.d. (s−1) |
| DESTconstants.txt | Various experimental parameters | Fit type (integer from 0 to 7 and - 1, see fit descriptions Table 1) B0field expressed as 1H Larmor frequency (MHz) Carrier frequency in DEST experiment (p.p.m.) DEST experiment sweep-width (Hz) DEST nucleus (3 for 15N, 2 for 13C, 1 for 1H) Relative weighting factor for ΔR2 values in fit optimization (e.g., 0.5) Length of DEST saturation pulse (s) Make plots (1 for yes, 0 for no) Save plots to file (1 for yes, 0 for no) Optimize parameters (1 for yes, 0 for no; i.e., if 0 just simulate with the initial parameter value and generate output) Optimize dark-state resonance offset chemical shift (CS; 0 for no, same CS as light state, 1 for yes, use a single residue-specific dark-state offset for all dark states, 2 use a separate residue-specific CS for each of two dark state) Values of R1 of dark states (0 to assume R1 in the dark state is uniform rate of 0.5 s−1, 1 to use position-specific R1 for dark states equal to user provided R1 in the NMR-visible state) |
| params1.txt | Various kinetic and relaxation parameters for McConnell model fitting | See Table 3 |
| normalize.txt | Scaling factor to manually normalize data points | Residue number, number by which to multiply auto-normalized DEST data to achieve desired normalization |
| folded.txt | Correction for aliased resonance positions | Residue number, integer number of times resonance position provided in dest.txt column 2 is aliased (positive integer for aliased downfield, negative for aliased upfield; where aliased downfield indicates that actual resonance position is downfield of spectral window) |
| darkoff.txt | Dark state CS, initial guess | CS (p.p.m.) for each data point in dest.txt in the same order, if the option to optimize CSs in the dark state is specified in DESTconstants.txt |
| darkoff2.txt | Dark state 2 CS, initial guess | CS (p.p.m.) for each data point in dest.txt in the same order, if the option to optimize CSs of two dark states independently is specified in DESTconstants.txt |