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R2R1_DIFFUSION

The program r2r1_diffusion uses the approach of Tjandra, et al. [J. Am. Chem. Soc. 117:12562-12566 (1995)] to determine the diffusion tensors for spherical, and axially-symmetric motional models from experimental nitrogen-15 spin relaxation data. Analysis of a fully anisotropic diffusion tensor has not yet been implemented. The program quadric_diffusion can be used to evaluate an anisotropic diffusion tensor in the limit of small anisotropy.

Usage: r2r1_diffusion control_file
The control_file contains the following information:
#_of_entries (in the r2r1_file) spectrometer_field (MHz) #_of_simulations
D_isotropic Dpar/Dper theta phi
axial_ratio_low axial_ratio_high #steps
r2r1_file_name
input_pdb_file_name
output_pdb_file_name (for axially symmetric model)
D_isotropic, Dpar/Dper, theta and phi are initial estimates of the elements and orientations of the diffusion tensor. D_isotropic is the only required entry; Dpar/Dper, theta and phi can be set to 1.00, 0.0, and 0.0 respectively. Ratio_hi and Ratio_low set limits on Dpar/Dper for grid search. Nsteps is the number of steps of grid searching to perform.

The r2r1_file contains the R2/R1 ratios, in which R2 and R1 are the spin-spin and spin-lattice relaxation rate constants for 15N or 13C spins. The r2r1_file contains one line for each residue to be analyzed. Each line contains the following fields:
residue_number r2/r1_ratio r2/r1_uncertainty
For both the control_file and r2r1_file, lines starting with "#" are ignored. The residue number in the r2r1_file must match the residue number in the input_pdb_file.

For each model (spherical, and axially-symmetric diffusion), the diffusion tensor and Euler angles are output. The chi-square and F statistics are calculated for comparing models. The program also returns the predicted effective diffusion constant for each residue and the squared residual from the fitting process. For diagnostic purposes, spherical harmonic functions of the NH bond vector (in the diffusion reference frame) are also output.

For axially symmetric diffusion model, the structure in the input_pdb_file is rotated to the diffusion frame. To be meaningful, prior to analysis, the center of mass of the molecular structure should be translated to coordinate origin by using the program pdbinertia.


Updated 9/23/97 by Arthur G. Palmer (agp6@columbia.edu)