AUTO Information

Welcome to a tutorial on the usage of the program AUTO.

AUTO is a suite of programs designed to automatically index and process electron diffraction patterns. These programs were designed to facilitate the automatic processing of electron diffraction pattern with particular interest to those acquiere using a slow-scan CCD camera. Becuase these cameras introduce a number of artefacts into the electron diffraction patterns, special programs were developed to deal with them. For instance, the patterns have a spike running throuh the central beam of the pattern, and several high-intensity pixels can be found that were caused by x-ray photons. The latter can originate from the gun or the CCD camera area, or can be from cosmic origin. Either way, they have to be removed.

AUTO consists of 7 programs written in FORTRAN 77, which are embedded in C shell scripts, which allows calling these programs from the command line and passing arguments to the programs. The electron diffraction pattern - indicated by the upper left rectangle - is processed by AUTOCENT, RBS, AUTOZERO, FIX_BAD_PIXELS, and AUTOINDEX. ALl programs are indicated by diamonds. The coordinates of the central beam and the lattice vectors are written into the MRC-header of the pattern. Next, the raw pattern is processed by GINTEN after which CHECK_SPOTS will remove bad reflections resulting in a list of reliable intensities (lower right rectangle).

AUTO requires at least 7 arguments to start processing. An example is given below:

	r4001: 1045 > auto cc.img.Z 9 p 9 20 "CC-gluc @ 45 degr.; JSB paper" 450

where the file is called cc.img.Z (compressed), the threshold for AUTOINDEX is 9, the Ewald sphere curvature-correction is positive, the rasters for the reflections and the background used in GINTEN are 9 and 20, respectively, a text field describing the pattern, and the maximum radius measured from the posotion of the central beam out to which AUTOINDEX and GINTEN should process the pattern.

The are 3 optional arguments, which tell AUTO at what location the central beam is, and whether or not AUTO should delete the pattern after is has been processed by FIX_BAD_PIXELS.

Below is the entry point to the tutorial on this entire procedure pertaining to the usage of the program AUTO.

Download AUTO

Continue with the tutorial.

Acknowledgments.

Back to the previous document on AUTO