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denzoindex: Find unit cell using Denzo from rotation images

The "denzoindex" program calculates a unit cell from a series of rotation images using Denzo, without any GUI interaction.

Usage

The program is invoked by the command line:

denzoindex [options] <"make" or kcdfilenames>

The "kcdfilenames" can be standard KCD files (not compressed). They should represent a single series of successive rotation images. If no "gui" option is specified, the default files are the first scan from "i*.kcd". If the "gui" option is specified and no ".kcd" files are given, the images can be selected using a GUI. Alternatively, "make" can be specified to first measure images and only then interpret them. Many options are available to control the way the images are measured.

The program will write a file "peaks.list" corresponding to peaks located in each image. It will then run the "denzo" program to find the cell, and integrate the frames to write ".x" files that contain the unit cell information (and integrated intensities). This information can be used by the programs in the collect suite.

Options

gui: Use a "gui" to ask for filenames, and follow the process in a "gui" environment.

The following options are available in combination with the "make" argument (and silently ignored if "make" is not specified):

dx=#: Crystal to detector distance (in mm) to use for the measurement.
degreetime=#: The exposure time (in seconds per degree) for the measurement.
frameangle=#: The frame angle (in degrees) to use for the measurement.
scanrange=#: The total scan range (in degrees) for the measurement.
theta=#: The theta position (in degrees). Normally 0, but for very small cells you might want a theta offset.
kv=# and ma=#: The generator setting to go to before starting the measurement. If no generator setting is given, the generator is automatically powered up to standard settings if necessary.
powerdown: Requests an explicit power down of the generator after the measurement.

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