Imcadr Manual

NAME

imcadr - center a crystal using diffraction rastering

SYNOPSIS

imcadr [--best-score-cutoff=number] [--cell-size=size]
       [--conf-file=file] [--debug-file=file] [--exp-time=number]
       [--help] [--high-res-cutoff=number] [--low-res-cutoff=number]
       [--min-signal-height=number] [--min-spot-area=number]
       [--no-chase] [--scoring-pkg=package] [--server] [--step-scan]
       [--version] [--weak-diff] [--zx-first] [--zx-mask=mask]
       [--zx-pre-clip-size=size] [--zx-size=size] [--zy-mask=mask]
       [--zy-pre-clip-size=size] [--zy-size=size] [directory]

DESCRIPTION

Imcadr centers a crystal using diffraction rastering.

If no options are specified, a GUI is displayed.

If the --server option is specified, Imcadr runs in server mode using the standard input and standard output streams for a text communication protocol. All other options, except for --conf-file and --debug-file, are ignored.

If the --server option is not specified but other options are, Imcadr requires that the exposure time, cell size, and at least one of the raster sizes be specified. Imcadr executes the crystal centering immediately without user input.

If directory is specified, it indicates the directory where raster images will be written. If omitted and no options are specified, an installation-dependent default location is used. If the installation-dependent default location does not exist, the user's home directory is used. If omitted and options are specified, the current working directory is used. directory is ignored when the --server option is used.

The options are as follows:

--best-score-cutoff=number

Abort centering if the best score of a raster is <= number.

--cell-size=size

Specify the raster cell size to be size (WIDTHxHEIGHT) in micrometers.

--conf-file=file

Read the configuration from file. The system-wide and user configuration files will be ignored.

--debug-file=file

Write debugging output to file.

--exp-time=number

Specify the exposure time for each raster cell to be number seconds.

--help

Print a help message and exit (also -h).

--high-res-cutoff=number

Specify the diffraction high-resolution limit to be number angstroms.

--low-res-cutoff=number

Specify the diffraction low-resolution limit to be number angstroms.

--min-signal-height=number

Specify the diffraction minimum signal height to be number sigma.

--min-spot-area=number

Specify the diffraction minimum spot area to be number pixels.

--no-chase

Disable best-score chasing. Best-score chasing results in a positional translation of the raster in the direction of the cell with the best score if it is on an edge. This is an attempt to find an even better score in an adjacent cell outside of the initially specified raster region. When disabled, no chasing (shifting) is performed.

--scoring-pkg=package

Use package to score raster cells. The supported values are labelit and dtrek. The value dstartrek is deprecated; it is an alias for dtrek.

--server

Run in server mode.

--step-scan

Use step-scans instead of fly-scans.

--version

Print the version number and exit.

--weak-diff

Indicate that the crystal is a “weak diffracter” (i.e. yields a low-resolution diffraction pattern). Note that this option is deprecated; instead, use options such as --high-res-cutoff to specify analysis parameters directly.

--zx-first

Rasterize the ZX raster first and the ZY raster second. This option is ignored if the --zy-size and --zx-size options are not both specified. If omitted, the ZY raster is rasterized first.

--zx-mask=mask

Mask out the ZX raster cells according to mask (ROW:COL[,COL...][;...]) where row and column indices start at 1. This option requires the --zx-size option.

--zx-pre-clip-size=size

Indicate that the ZX raster size was size (WIDTHxHEIGHT) in cells before being clipped. A message indicating clipping will be written to the result file. This option requires the --zx-size option.

--zx-size=size

Specify the size of the ZX raster to be size (WIDTHxHEIGHT) in cells. If omitted, the ZX raster is skipped.

--zy-mask=mask

Mask out the ZY raster cells according to mask (ROW:COL[,COL...][;...]) where row and column indices start at 1. This option requires the --zy-size option.

--zy-pre-clip-size=size

Indicate that the ZY raster size was size (WIDTHxHEIGHT) in cells before being clipped. A message indicating clipping will be written to the result file. This option requires the --zy-size option.

--zy-size=size

Specify the size of the ZY raster to be size (WIDTHxHEIGHT) in cells. If omitted, the ZY raster is skipped.

EXIT STATUS

0

Success.

>=1

Failure (syntax or usage error; configuration error; unexpected error).

2

Best score in raster <= best-score cutoff.

ENVIRONMENT

IMCADR_CONFIG

The location of the user configuration file. If not set, Imcadr will look for ~/.imcadr.conf. If that is not found, Imcadr will check whether the XDG_CONFIG_HOME environment variable is set, and, if it is, will look for $XDG_CONFIG_HOME/imcadr/config. Otherwise, Imcadr will look for ~/.config/imcadr/config.

FILES

~/.imcadr.conf

User configuration file.

/usr/local/etc/imcadr.conf

System-wide configuration file.

EXAMPLES

To run with a 0.25 second exposure time per raster cell, a 70x35 micrometer cell size, a 5x5 ZY raster, and a 3x5 ZX raster, saving images to the current working directory:

$ imcadr --exp-time=0.25 --cell-size=70x35 --zy-size=5x5 --zx-size=3x5

SEE ALSO

imcadr.conf(5)