Calculate alignment tensor using singular value decomposition (SVD) given RDC (or PCS) values and one or more molecular structures. Also, optionally create a plot of observed vs. calculated RDCs.
Usage: calcTensor [options] <rdc table> <pdb file1> [<pdb file2> ...]
where option is one or more of:
-psf <psf filename(s)> - One or more PSF filenames. If more than one
filename is specified, they must be either
space-separated and enclosed in quotes, or
colon-separated.
If this option is omitted, the PSF information
is auto-generated.
-showRDCs - Print out back-calculated RDC values for the
final structure on the command-line.
-normType <normType> - RDC normalization. One of NH, CH or none
[default value: NH].
-correctSign - Use the proper sign for the 15N gyromagnetic
ratio. By default the sign is taken to be
positive. Please see Xplor-NIH documentation
for the rdcPotTools module.
-useDistance - Include 1/rAB^3 distance dependence in RDC
calculation. By default this is only enabled
if a non-bonded RDC type is detected.
-maxDa <value> - Set the maximum absolute value of Da
[default: 50].
-fitSel <atom selection> - Atom selection used to fit structures before
alignment tensor calculation.
-fitallExps - Use all input RDCs (including cross-validated
ones) to calculate the alignment tensor
[default: non-cross-validated RDCs].
-genNames <sel1> <sel2> - two atom names used to generate assignment
table to be used to back-calculate RDCs. The
generated table will not include RDCs from the
input rdc table, and the observed RDCs will be
set to 0. These RDCs are not used to determine
the alignment table.
-txtNames <name1> <name2> - two atom names used to generate restraints from
space-separated columnar restraint files ending
with .txt or .dat suffixes. These default to
N and HN.
-ensemble - Treat the input structures as a true solution-
phase ensemble of structures which are not fit
together.
-ensWeights <weights> - a colon- or space-separated list of weights to
use for population values of individual
ensemble members.
-rdcWeights <weights> - Colon- or space-separated list of weights used
to weight RDC experiments relative to each
other [defaults to 1 for each].
-svdTol <value> - discard singular values less than value times
the average of the singular values.
-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 backcalculated RDCs
are printed with the calculated tensor. A
NEF restraint file can also be specified,
separated by a colom from the saveframe
containing RDC restraints, if there is more
than one.
-subSel <atom selection> - Specify a subset of RDC/CSA restraints used to
perform SVD. The atoms chosen are the
intersection of this atom selection and the
strings specified in the ASSIgnment statements.
-crossSel <atom selection> - Specify a subset of cross-validated RDC/CSA
restraints used for analysis. The atoms chosen
are the strings specified in the ASSIgnment
statements. If not provided, this value
defaults to that given by the -subSel option.
-getTags - Return RDC values, along with coordinate data.
-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.
-addUnknownAtoms - if specified, add missing atoms.
-noUseErrs - Do not weight the terms with 1/err in the SVD
calculation.
-DaRh <Da> <Rh> - specify Da and rhombicity. In this case, only
the alignment tensor orientation is determined.
Currently, this only supports tensor
calculation from a single structure.
-plot - Produce a plot of calculated vs. observed
RDCs. Error bars indicate input experimental
errors and the spread between calculated
structures' RDCs. If a point in the plot is
clicked, the first atom selection will be
printed so that outliers might be identified.
-plotLabels - At each point on the correlation plot, place a
label corresponding to the residue number of
the first atom selection.
-plotVsResid - display a plot of calculated and observed RDC
values as a function of residue number.
<rdc table> is one or more space- or colon-separated files containing
observed RDC values in XPLOR-SANI, space-separated columnar or NEF
format, and pdb file1, ... are one or more PDB coordinate files. The
NEF format is signified by the rdc table filename ending in
".nef," and if it includes more than one saveframe with RDC
restraints, the saveframe name should be specified immediately
following the filename, separated by a colon. If the filename ends in
.txt or .dat, a column-separated format is assumed with columns of
resid, obs and err, and the associated atom names are specified using the
-txtNames option. Files with other suffixes are assumed to be in
XPLOR-SANI format.
By default, input RDCs are subsequently normalized relative to the one-bond
NH pair. To change this behavior use the option -normType.
By default, the output is the optimal alignment tensor's
Da and rhombicity, the RDC fit root mean square deviation and R-factors,
defined by Eqs. 5 and 3 of Clore+Garrett, JACS 121, 9008 (1999).