calcTensor
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).