___________________________________________________________ NMRPipe: the Multidimensional Spectral Processing System Based on UNIX Pipes Feb 10, 2006 ___________________________________________________________ NMRPipe provides comprehensive facilities for Fourier processing of spectra in one to four dimensions, as well as a variety of facilities for spectral display and analysis. It is currently used in over 300 academic and commercial laboratories. For details on the system's design principles and capabilities, see the electronic reprint of the J. Biomol. NMR paper describing NMRPipe. (http://spin.niddk.nih.gov/bax/software). The companion system NMRWish is a version of the TCL/Tk Window Shell "wish", with over 100 additional commands for spectral manipulation and spectral graphics, as well as a simple general purpose database engine. For information about the availability of NMRPipe, or about subscription to the NMRPipe mailing list, contact the author (delaglio@nih.gov). PROCESSING * Complete multidimensional processing schemes can be constructed as simple shell scripts, without the need to anticipate or explicitly specify data sizes. The dimensions can be processed and re-processed in any order, with the correct combination of real and imaginary data supplied automatically. * Spectral axis calibrations are maintained during all stages of processing, so that processing parameters can be specified in terms of spectral units where desired. * Comprehensive implementation of complex linear prediction (LP) and multi-dimensional maximum entropy method (nD-MEM) for reconstruction of truncated data, as well as complete and convenient inverse processing protocols required for their use. * Convolution-based and polynomial solvent subtraction are provided, as well as automated and manual baseline corrections. * Macro interpreter provides facilities for user-written processing functions in a subset of C. * The pipeline approach is intrinsically parallel and automatically takes advantage of multi-cpu configurations. In addition, explicitly parallel schemes can also be constructed for balanced partitioning of processing tasks. * Processed data can be used with well-known spectral analysis programs such as: o ANSIG (Per Kraulis, Pharmacia) o NMRView (Bruce Johnson, Merck) o PIPP (Dan Garrett, NIH) o XEASY (Christian Bartels et al.) NMRDraw * Interactive interface for inspecting 1D-4D FIDs, interferograms, and spectra. * Real-time manipulation of one or more 1D vectors within the viewed data, including pan, zoom, vertical scaling and offset, with 1D spectral graphics overlaid on 2D contour display. * Real-time phasing of one or more vectors for any dimension, with imaginary data reconstructed automatically as needed. * Facilities for interactive processing of individual vectors, and a script editor for construction of processing schemes. * Interactive peak editing, with an interface to automated 1D-4D peak detection via NMRWish. NMRWish NMRWish is a custom version of Tcl/Tk for use with the NMRPipe System. Tcl/Tk is a powerful and widely used command language which includes facilities for graphical interface creation and for communication between different applications; Tcl was introduced to the NMR community in the powerful package NMRView (Bruce Johnson, Merck). In addition to the usual features of Tcl/Tk, the special facilities of NMRWish include the following: * Extraction or projection of arbitrary spectral Regions of Interest (ROIs), with options for centering and alignment, as well as automatic unfolding and sign-adjustment. * Automated peak detection in 1D-4D, including options for identifying peaks due to random noise and truncation artifacts. * Multi-window spectral graphics, with complete support of the usual Tk graphics canvas facilities. * Scripts provide fully customizable PostScript output, including 1D and 2D extracts and projections, overlays, images, and strip plots. * A simple, general purpose database engine, capable of manipulating peak tables, assignments, and PDB format molecular coordinates. * General facilities for reading, writing, and manipulating binary data, including type conversion, general purpose vector processing, and access to NMRPipe processing functions. SPECTROMETER FORMAT CONVERSION * Conversion facilities specifically for Varian and Bruker binary time-domain data are provided, as well as general purpose facilities accommodating most other formats. All data is converted to a common format with a uniform organization of real and imaginary points. * The conversion commands can read or write data from a command pipeline rather than a file, allowing such capabilities as conversion of compressed data, conversion of input data dispersed over more than one file, and processing schemes which go directly from spectrometer format to processed result. * Dedicated interactive Varian conversion interface reads the procpar file and automatically extracts many acquisition parameters. * Dedicated interactive Bruker conversion interface reads and interprets pulseprogram and acq files to deduce many acquisition parameters. Full compensation for Bruker digital filter format is performed during conversion. * All conversion facilities support special options for complex acquisition schemes, including gradient-enhanced data (Rance-Kay/echo:anti-echo) and accommodation for interleaved data formats. UTILITIES * Facilities to display and adjust NMRPipe-format file header information. * Multi-dimensional lineshape fitting utility, including time-domain, frequency-domain, and hybrid models, and treatment of pseudo-3D data (e.g. relaxation series or coupling evolution data). * Generation of peak evolutions from volume summation or Fourier-interpolated intensity. * Facilities to simulate multidimensional time-domain and frequency-domain data from peak tables. * Algebraic combination of spectra and FIDs. * General purpose least-squares fitting utility with user-defined functions and Monte Carlo error analysis. * Summary statistics of data from spectra or text tables. * Principal Component Analysis (PCA) HARDWARE AND OPERATING SYSTEMS The list below shows current or previous UNIX versions of NMRPipe. In addition to these , a closely related commercial implementation for the WindowsNT operating system, called NT-NMRPipe, is also available. For information on specific versions, contact the author, Frank Delaglio, delaglio@spite.niddk.nih.gov. * Sun Solaris I (SunOS) * Sun Solaris II (System V) * Intel PC Solaris II * Intel PC Linux * SGI IRIX 4 * SGI IRIX 5 * SGI IRIX 6 * DEC Alpha * IBM R6000 * HP HP/UX * Convex * Cray EXAMPLE PROCESSING TIMES Benchmarks for (512*)(64*)(32*) Fourier Processing Hardware OS Application Time --------------------- --------- ---------------- Pentium II 400 Linux 48 sec SGI R10000 2 CPU IRIX 49 sec SGI R10000 IRIX 73 sec SGI R4000 IRIX 381 sec Pentium Pro 200 2 CPU Solaris 72 sec Pentium Pro 200 2 CPU Linux 82 sec Pentium Pro 200 2 CPU NT 144 sec Pentium Pro 350 NT 108 sec Pentium Pro 300 NT 174 sec Pentium Pro 200 NT 244 sec Sparc Ultra 10 Solaris 138 sec Sparc Ultra 1 Solaris 248 sec Sparc 10 SunOS 662 sec