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    Microscopic NMR imaging : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University
    (Massey University, 1987) Eccles, Craig David
    In the process of developing the imaging system it was necessary to write an extensive range of software. Our only access to the TI-980A was via a series of bit switches and so the first task was to write a hex monitor which would speed program entry. A fairly extensive software package was provided with the system for the purpose of performing NMR spectroscopy and so rather than rewrite FFTs etc from scratch much of this software (conveniently in the form of subroutines) was used by the imaging system. The Hitachi was supplied without any software apart from BASIC and MSDOS. IBM PC Fortran, Pascal and assembler were obtained which ran on this machine but because of graphics and I/O incompatibilities no graphics library was available. It was therefore necessary to write a number of 8088 assembly language routines to perform these essential functions. All those routines (such as image display, backprojections and FFTs) which required rapid execution were written in assembler and called as subroutines from Fortran (this programmers language of choice). Those routines for which speed is not a primary requirement or which are currently in the development stage have been written in Hitachi Basic. This volume is divided into 2 sections. The first part contains the TI-980A routines which are used to control the imaging experiment. The second contains listings and flowcharts for programs written on the Hitachi in Fortran, Basic and assembler.
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    PAW - the Protein Analysis Workshop for 2D nuclear magnetic resonance spectroscopy : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Physics at Massey University, New Zealand
    (Massey University, 1999) Lie, Wilford; Lie, Wilford
    An X Window-based software package for SGI workstations has been developed to process and assign NMR spectra. Special consideration has been given to the assignment of two-dimensional 1H NMR spectra of proteins. The program combines features from the packages PROSPA [Eccles 1995], EASY [Eccles 1991] and FELIX [Biosym 1995] as well as having its own capabilities. It allows simultaneous display of multiple toolboxes and spectra, which can be flexibly manipulated by mouse operations, command entries, and user-editable macros. NMR spectra can be processed either interactively or with macros containing commands with parameters. A unique filter that combines the exponential and sine-bell functions has been frequently used. A water suppression technique based on fitting averaged time-domain data, as well as an efficient algorithm for calculating fast Fourier transform and Hilbert transform [Eccles 1995] are discussed and implemented. NMR spectral assignment is done interactively in three steps: peak picking, spin-system identification, and sequence-specific assignment. The process utilises three peak lists: a raw-peak list that contains records of all possible peaks in a NOESY spectrum, a diagonal peak list that contains records of peaks that define a curve about which the spectrum is symmetric, and a cross-peak list that contains records of peaks that are assigned. Details of the peak-picking methods are discussed. By reference to a list of diagonal peaks, a common calibration problem caused by Bloch-Siegert shifts [Bloch and Siegert 1940, Ernst 1987] has been minimised. Automatically produced NOE summaries allow a quick identification of peaks that are unassigned or incorrectly assigned. The peak position and integration parameters can be calculated through non-linear curve fitting with Gaussians. NMR data processing and spectral assignment using the package has been completed for Caerin 4.1, a 23-residue protein. Linear-prediction has been applied to increase the spectral resolution. Detailed results for this protein are presented. The NOE summary of the sequential assignments indicates a well-defined secondary structure that is different from Caerin 1.1 [Wong 1996, 1997].