Xplor-NIH Helper Programs
The following helper programs are distributed with Xplor-NIH, and present in the bin subdirectory of the Xplor-NIH distribution. If the --symlinks DIR option to the configure script was used during installation, symbolic links to the programs will be present in the directory DIR. These options can be supplied to any Xplor-NIH command.
| xplor: | Invoke Xplor-NIH. Use the -py option for the Python interface. |
|---|---|
| pyXplor: | Invoke the Xplor-NIH Python interpreter. |
| tclXplor: | Invoke the Xplor-NIH TCL interpreter. |
| getBest: | Print out the filenames of the lowest energy structures listed in an Xplor-NIH .stats file. By default, all .stats files in the current directory are consulted. It can also be used to create symbolic links to these filenames. |
| seq2psf: | Generate a PSF file from a PDB file. This is only possible for PDBs with residues contained in Xplor-NIH's default topology database. |
| pdb2psf: | Generates a psf file from the given pdb file. The psf file is written to a filename derived the input filename. |
| targetRMSD: | Compute positional RMSD to a reference structure. |
| 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. |
| calcETensor: | Calculate an ensemble of SVD alignment tensors from an ensemble of structures and observed RDC values. The tensors are underdetermined. |
| 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). |
| domainDecompose: | |
| Given an ensemble of structures, find regions of structural similarity, using maximum-likelihood fitting. | |
| mleFit: | Fit structures and determine unstructured regions using the maximum likelihood methodology of D.L. Theobald and D.S. Wuttke, "THESEUS: Maximum likelihood superpositioning and analysis of macromolecular structures," Bioinformatics 22, 2171-2172 (2006). |
| calcSAXS: | Given a molecular structure, compute a SAXS or SANS curve, optionally fitting to experiment. Also compute optimal excluded solvent parameters (including boundary layer contribution). |
| torsionReport: | Generate report on all protein torsion angle values for one or more structure files. Reports generated for individual structures and averages. |
| findClusters: | This script clusters structures by their positional RMSD, using the given atom selection. |
| compareTensors: | Given two raw Saupe matrices specified in stdin, compute the normalized scalar product between the two tensors and the scalar product between axes. Also, compute angle of rotation between two axes. Reference: J. Sass et al. J. Am. Chem. Soc. (1999) 121:2047-2055. |
| aveStruct: | Given an ensemble of structures, compute an unregularized average structure and report per-atom RMSD. |
| ens2pdb: | Converts an ensemble of structure files to a single PDB, with structures separated by MODEL records. The SEGID field is written to the ChainID field so it must be, at most, a single character. The result should be acceptable for PDB submission. |
| 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). |
| contactMap: | Generate contact map from one or more pdb files. |
| ramaStrip: | Perform Ramachandran analysis on each specified residue. Print contours levels containing 98% and 99.8% of all high-resolution structure. For each structure specified, plots a blue point if the associated phi/psi value lies inside the 99.8% contour, and a red point otherwise. For each structure, also print out all violated phi/psi values on stdout. For a description of the structure database and generation of the density surface, please see G.A. Bermejo, G.M. Clore, and C.D. Schwieters, Protein Science 21, 1824-1836 (2012). |
| scriptMaker: | Generate an Xplor-NIH script using a graphical user interface (written by Alex Maltsev). |
| calcDimerConc: | Given subunit concentration and Kd, return dimer and monomer concentrations |
| convertTalos: | Convert Talos+ and talos-N output to phi/psi torsion-angle restraints for use in Xplor-NIH. The allowed range of torsion angles will be all those from the ten Talos+/TalosN hit values. This script will produce restraints for all residues which for which Talos+/N classifies its predictions as "Good" or "Strong". By default, hits are ignored if Talos+/N give them zero weight. |
| runSparta: | Compute the backbone chemical shifts, and optionally fit to experimental values. This uses a modified version of "SPARTA+: a modest improvement in empirical NMR chemical shift prediction by means of an artificial neural network Yang Shen and Ad Bax," J. Biomol. NMR, 48, 13-22 (2010). |
| plotLog: | Create a two dimensional plot from X-Y data. |
| calcPSol: | Compute the solvent PRE given a molecule structure and a restraint list. |
| calcPRE: | Given a molecular structure and a PRE restraint table, back-calculate PRE values, and optionally plot the observed and calculated values as a function of residue number. The convention used in this helper program is that the paramagnetic tag is listed in the first selection, while the measured residues are listed in the second selection. |
| pbsxplor: | Generate a PBS script and submit it as a PBS job using qsub. |
| slurmXplor: | Generate a SLURM script and submit it as a s job using sbatch. |
| idleXplor: | Edit and run Xplor-NIH scripts. |
| genSurf: | Generate surf output for VMD. |
| hbScore: | Perform H-Bond scoring on each input file. |
| energyPlot: | Read an Xplor-NIH output file from stdin and plot or print energies printed during dynamics and minimization. Example: energyPlot < script.out |
| detChirality: | Determine the chirality of centers in the specified PDB file. |
| headerHelp: | Print out documentation for the specified header term. |
| calcSA: | Compute solvent-accessible surface area (in Angstroms) for the specified atoms or residues of one or more PDB files using the algorithm in A. Varshney et al. IEEE Comput. Graphics Appl. 1994, 14, 19-25. |
| analyzeRepel: | Analyze coordinates for RepelPot nonbonded clashes. |
| calcPr: | Given a PDB, compute the P(r) due to adding MTSL tags at the specified residues. |
| calcTrace: | Given a PDB, compute the DEER trace arising from signal due to adding a pair of MTSL tags added at the specified residues. |
| evalDists: | Print out fit of given distance restraints to the specified structures. |
| evalDihedrals: | Print out fit of given dihedral restraints to the specified structures. |