domainDecompose
Given an ensemble of structures, find regions of structural similarity, using maximum-likelihood fitting.
Usage: domainDecompose [options] <structures to fit>
where the structures to fit is a space-separated list of pdb filenames.
Options are zero or more of:
-selection <string> - atom selection specifying which atoms to use in the
fit [default value: name CA]
-mSelect - specify method of regularizing the inverse of the
covariance matrix -
if 0 use perturbative approach - add a small value to
the diagonal. If 1 use diagonal elements as
``eigenvalues,'' and follow the scheme of Theoboald
and Wuttke. [default: 0]
-smallestDomain - number of resideus in smallest allowed domain
[default: 20]
-verbose - cause intermediate values of log likelihood and
RMSD to be printed.
-rmsdThreshold <value> - specify the RMSD value for determining whether
an atom is in an ordered region [default: 3.500000
angstrom]
-rmsdTolerance <value> - specify the ML RMSD value for determining whether
the fit using the current set of atoms is
well-defined [default: 1.500000 angstrom]
-deltaThreshold - how much to reduce the rmsdThreshold on successive
iterations of fitting. [0.5 Angstrom]
The algorithm is described in:
J.J. Kuszewski, R. Augustine Thottungal, G.M. Clore and C.D. Schwieters, "Automated error-tolerant macromolecular structure determination from multidimensional nuclear Overhauser enhancement spectra and chemical shift assignments: Improved robustness and performance of the PASD algorithm," J. Biomol. NMR 41, 221-239 (2008).