calcSARDC
Compute the alignment tensor for the input structure(s) assuming partial steric alignment. The required input experimentally observed RDCs are used to appropriately scale the tensor. The calculated version of the RDCs can be output in printed form (-showRDCs option) and in a correlation plot with the observed values (-plot option). This function returns a tensor (and calculated RDCs) that is (are) inaccurate if the input observed RDCs do not stem from a steric alignment mechanism.
This implementation uses the method described in: J-r. Huang and S. Grzesiek, ''Ensemble Calculations of Unstructured Proteins Constrained by RDC and PRE Data: A Case Study of Urea-Denatured Ubiquitin'', J. Am. Chem. Soc. 132, 694-705 (2010).
Usage: calcSARDC [option] -table <RDC table> <PDB files>
The RDC table can be a single file name or a space- or colon-delimited list of files.
Options:
-psf <psf filename> - Specify a PSF filename. If omitted, PSF info is
automatically generated from the PDB file.
-subSel <atom selection> - Specify a subset of RDC restraints used in
back-calculation.
-crossValidate <files> - Colon- or space-separated list of files with
XPLOR SANI-style assignment statements of
measured RDC values which are not used for
fitting, but for which back-calculated RDCs
are printed with the calculated tensor. Use of
this term implies -showRDCs.
-ensWeights <weights> - Colon-separated list of weights to use on
structure ensemble members.
-ensWeightsRegexp=value - Regular expression used to identify the
beginning of the EnsWeights section of PDB
REMARKs. This should be: 'EnsWeights.*\{'.
The weights obtained using this argument are
multiplicatively combined with those from the
-ensWeights option.
-ensWeightsTerm=value - String used to identify ensemble weights from
remarks section of the PDB header. This is
the name of a potential term. The weights
obtained using this argument are multiplicatively
combined with those from the -ensWeights option.
-showRDCs - Print out all back-calculated RDC values to
the terminal.
-aveType <type> - Specify the type of averaging when an atom
selection specifies more than one atom. The
choices are: sum, average, and pairwise. The
default value is pairwise.
-noUseSign - Do not consider the sign of the RDC when
comparing observed with computed values.
-noScaleOptimize - Disable optimization of tensor scale factor.
-plot - Produce a plot of calculated vs. observed RDCs.
Error bars indicate input experimental errors and
the spread between calculated structures' RDCs.
-singleEns - Normally, specification of multiple PDB files
denotes that each structure should be fit
separately. However, if a filename is a glob,
it is treated as an ensemble (it may be helpful to
set -o glob in yourshell to avoid expanding them
too early). If -singleEns is specified, the files
specified are treated as an ensemble regardless.