calcDaRh
Estimate the alignment tensor's Da and rhombicity solely from input RDC values (i.e., no structural information) via a maximum likelihood method, assuming isotropically distributed internuclear vectors within the molecule. Input RDC tables use default Xplor-NIH format, unless the filename ends with ".txt" or ".dat", in which case a column-separated format is assumed, with columns of residue no., RDC value and RDC error, respectively.
This implementation uses the maximum likelihood method described in: J.J. Warren and P.B. Moore, ''A Maximum Likelihood Method for Determining Da(PQ) and R for Sets of Dipolar Coupling Data'' J. Magn. Reson. 149, 271 (2001).
Usage: calcDaRh [options] <structure info> <dipolar coupling tables>
One of -psf, -seq or -pdb must be specified. However, structural information is not used in the fit. The file is used to assess the internuclear vector type.
By default, input RDCs are subsequently normalized relative to the one-bond NH pair. To change this behavior use the option -normtype.
At exit, the powder pattern corresponding to the calculated Da and rhombicity, and a crude histogram of input RDC values is output in a separate file. The file has three columns corresponding to RDC value histogram count powder pattern intensity.
Options:
-pdb <pdb file> - specify pdb file |
-psf <psf file> - specify psf file | one required
-seq <seq file> - specify file containing a sequence. |
-segid <segid> - specify the segid. Only useful if the sequence is
input using -seq
-startResid <resid> - specify the first residue number of a sequence.
Only useful if the sequence is input using -seq
-error <error spec> - specify the experimental error [default value: 1]
A Gaussian with this width is convolved with
the powder pattern in the maximum likelihood
calculation. If multiple RDC tables are specified,
differing error values can be supplied for each
table by specifying multiple numbers separated by
a colon, e.g., -error 1:5:3
-normtype <spec> - specify how to handle normalization of different
experiments. spec can be NH, CH, or none
[default: NH]
-binsize <num> - specify the bin size used for the histogram. This
does not affect the calculation of Da, Rh.
-histfilename <file> - specify the filename for the output histogram
[default: histogram.out].
-verbose - print values of most likely Da, Rh as they are
calculated.
-help - print this message.