SPECTRA: a system for processing electron images of crystals

SPECTRA is a program system that combines well tested and familiar algorithms and advanced graphics tools for (i) the display and indexing of the Fourier transform of images of crystalline specimens, (ii) refinement of the reciprocal lattice, (iii) output of amplitudes and phases of reflections and (iv) lattice distortion correction through cross-correlation map analysis. Because of the ease of identifying and indexing reflections, the user can include many reflections for reciprocal lattice refinement, leading to more accurate lattice determination. Automatic indexing is much faster than entering indices by hand, with less operator error. The user can run the procedure that corrects for lattice distortions with either standard parameters or storable parameters tailored to a particular specimen. SPECTRA's primary function is as a control program which acts as an interface between existing programs and the user. It was written in C with routines for the display, user interface and peak list search. Communication between the separate processes that make up SPECTRA is via the UNIX pipe mechanism and command files, the latter so that users may run, test or replace them or even run them as stand-alone programs outside this system.