Table 2.

Input parameters for DYNAMICS

Parameter or data array name (case sensitive)	The meaning	Data format/structure	Required?
freq	1H frequency, in MHz, could be several (Nfreq) frequencies, if data at multiple fields	vector of length Nfreqa	Yes
r11 (if single field) or several arrays r11, r12, etc generally: r1i where i=1,2,…,Nfreq	R1 data for Nres residues at a given frequency i	Array Nresb ×3: [Residue# R1c σR1c]	Yes
r21 (if single field) or several arrays r21, r22, etc generally: r2i where i=1,2,…,Nfreq	R2 data for Nres residues at frequency i	Array Nres×3: [Residue# R2c σR2c]	Yes
r31 (if single field) or several arrays r31, r32, etc generally: r3i where i=1,2,…,Nfreq	NOE data for Nres residues at frequency i	Array Nres×3: [Residue# NOE σNOE]	Yes
vNH	NH-vectors (normalized) for Nres residues	Array Nres×4: [Residue# x y zd]	Only for anisotropic diffusion models (kovrl=1 or −1)
csa	CSA values for Nres residues	Array Nres × 3: [Residue# CSAe σCSAe]	Only for fixed site-specific CSA (kcsa=−1). If kcsa=0, the program will ask you
TAUc	Overall rotational correlation time, σc, in ns	Scalar or vector	Yes. If TAUc is missing in the workspace, the program will ask you to input it manually
Dz2Dx, Dy2Dx	Ratios of the principal values of the diffusion tensor (Dz/Dx, Dy/Dx)	Scalars	Only for anisotropic diffusion models (kovrl=1 or −1). The program will ask you to input them manually
alpha, beta, gamma	Euler angles {α,β,γ}, in degrees that define the orientation of the diffusion tensor axes with respect to the protein coordinate frame	Scalars or vectors	Only for anisotropic diffusion models (kovrl=1 or −1). The program will ask you to input them manually
Ct, Kd	Molar concentration of the protein (Ct) and the dimer’s dissociation constant (Kd), both in mM	Scalars	Only for monomer-dimer equilibrium model (kovrl=2). The program will ask you to input them manually
kovrl	Flag indicating various rotational diffusion models	=0 for isotropic (default); =1 for axially symmetric; =−1 for fully anisotropic; =2 for monomer-dimer equilibrium	Only for non-isotropic motion, otherwise set to 0 by default
kcsa	Flag for selecting various CSA options	=0 for fixed uniform CSA (default); =−1 for fixed site-specific CSA; =1 to fit site-specific CSA	Only for non-uniform CSA model, set to 0 by default
kplot	Flag to suppress (0) or allow (1) visual output in a form of data plots	=0 =1 (default)	Only for suppressing plot, otherwise set to 1 by default
kfig	Flag controlling figure numbers for plotting the results	=0 open a new figure (default); =−1 plot to the same figure; otherwise figure #=kfig	Only to output to a specific figure#, otherwise set to 0 by default
ML_ver	Matlab version	e.g. for Matlab version 7.01, ML_ver = 7.0	Set manually or let the program determine

^aN_freq= number of frequencies in the freq list

^bN_res= number of residues in the list. If data for some residues are unavailable, do not include these residues in the list or use NaN (see footnote c)

^cThe values of relaxation rates R₁, R₂ and their experimental errors, σR₁, σR₂, should be in 1/sec, the values of NOE and the experimental error, σNOE, are dimensionless. If for a given residue the relaxation parameter (R₁, R₂, or NOE) is not available, input NaN (“non-assigned-number”) in the corresponding position (second column) in the array.

^dx,y,z should be coordinates of a unit vector in the direction of the NH bond (can be obtained by running an auxiliary program pdb2nh, see Section 3.6.1)

^eCSA values and their errors (σCSA) should be in ppm