Processing of Electron Diffraction Patterns

***  Preliminary

        pds2mrc or convgatan            convert to MRC format
        mrcdisp filename		to view pattern - refine
                                        lattice parameters and determine center
        prnimg filename			to obtain postscript output for printing
        ghostview prnimg.ps		to preview postscript output
	lp prnimg.ps			to send output to printer

***  Processing in individual patterns

        backauto(ccd)           to determine and subtract radial background
                        input:  *.pat,center,
                        output: *.crt,*.bck,*.ycr,background.plt

        autoindex               to determine lattice parameters a* b*
                        input:  *.crt (background subtracted image)
                        output: *.index,autoindex.plt,lattice parameters, raster sizes

        pickauto(ccd)           to refine lattice and integrate intensities
                        input:  *.pat,*.bck,*.ycr,(*.crt for auto lattice and 
                                raster parameters),lattice and raster param
                        output: *.lst,Friedel R factor, tilt axis/angle

        p1toc2                  to convert p1 lattice of pickauto to c2
                        input:  *.lst
                        output: *.spt

***   Processing of Tilt Series

        pickpeaks               to sort data from tilt series allowing peak id
                                    and convert latt param to c2
                        input:  *.spt, tilt axis/angle
                        output: latt param (c2), sorted list of reflections (h,k,int,z*)
                                 "calst" this file used as input to linefit

        cstarfit                to determine c* direction, tilt axis
                        input:  tilt angles, latt parameters for all films in series
                        output: c* direction, EM tilt axis, total xtal tilt axis/angle
                                  parameters OK for MERGEDIFF

       /
      |  srchtaxs                MathCad program to find EM tilt axis and cstar direction
      |  tangles                 MathCad program to find total xtal axis/angle 
       \                input:  same as cstarfit
                        output: same as cstarfit tilt axis appropriate for MERGEDIFF



        linefit                 to find a*, b*, c* lattice vectors best fit to 
                                        observed peaks
                        input:  c* direction (tilt axis 1st film), EM tilt axis/ang
                                 latt param, "calst" (edited to mark peaks)
                                 
                        output: a*,b*,c*,beta*, resid for fit, "positions"

        tseriesfit              to plot data from tilt series to compare check fit
                        input:  "positions"         
                        output: tseriesfit.plt



***  Merging of Patterns into 3D

        mergediff3d             to merge individual films into 3D data set
                        input: *.spt, total tilt ang/axis, possibly reference data
                        ouput: merged list of reflections, statistics for merging

        syncfit3d               to fit curves to merged list of reflections
                        input: merged list of reflections (h,k,int,c*), parameters for fit
                        output: *.crv (curves for mergediff), *.cfs (sync coeff), plotfile

        pltsync3d               to plot curves with data from syncfit
                        input:  plotfile from syncfit
                        output: *.plt