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
Usage: r2r1_diffusion control_file
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 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
- output_pdb_file_name (for axially symmetric model)
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:
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.
- residue_number r2/r1_ratio r2/r1_uncertainty
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