alignlog(1) General Commands Manual alignlog(1) NAME alignlog - extract data from tiltalign log file SYNOPSIS alignlog options [a | b | log_filename] DESCRIPTION This Python script extracts useful sections from the output of Tiltal- ign(1). One or more options may be entered in any order; if multiple options are given, the different sections are printed out in the order given. If no filename is entered, alignlog will attempt to extract sections from the file align.log. If a or b is entered instead of a filename after the options, then sections will be printed from aligna.log or alignb.log, respectively. OPTIONS Alignlog uses the PIP package for input (see the manual page for pip). Options can be specified either as command line arguments (with the -) or one per line in a command file (without the -). Options can be abbreviated to unique letters; the currently valid abbreviations for short names are shown in parentheses. -m Mappings: print variable mappings -e Errors: print errors and ratio of measured to unknowns -s Solution: print the alignment solution for each view -l Local: print the location and size of each local area, the num- ber of fiducials on each surface, and the mean residual. -c Coordinates: print the 3-D coordinates of the fiducials -r Residuals: print large residuals -a Angles: print planar fits and recommended change in angles -b Beam tilt: print F values (RMS errors) from beam tilt search -w Robust weighting: print output from robust fitting and weighted mean residuals -help (-h) OR -usage Print help output -StandardInput Read parameter entries from standard input EXAMPLES Print solutions and errors from align.log: alignlog -s -e Print 3-D coordinates and angle recommendations from alignb.log: alignlog -c -a b AUTHOR David Mastronarde, mast at colorado dot edu SEE ALSO tiltalign BUGS IMOD 4.11.0 alignlog(1)