Interactive DPS/Mosflm/CCP4 Data Processing Version 2.01
General information, and starting the system
This system may be used to process images from a variety of area detectors (see Detector types for a list). The user interface has been developed through a collaboration between Area Detector Systems Corp. and Cornell and Purdue Universities. The working routines include "DPS" programs from Purdue and Cornell, an image display program from ADSC, and the Mosflm/CCP4 package from Andrew Leslie and the CCP4 group.
Development of the software is continuing. This documentation is for Version 2.01, released August 2001. Comments on the programs themselves, and on this documentation, are welcome; send them to Marian Szebenyi.
To process a set of data, type "process" for an initial run. If you already have a parameter file (created by a previous run of the program), you can type "process name", where "name.param" is the name of the parameter file. Process is a script that copies the necessary shell scripts ("command files") from a standard location to the current directory (if they're not already there), starts up processing_gui, and loads the specified parameter file, or a standard prototype if no filename is given. The main interactive window, part of which is shown here, will come up.
Processing_gui stores information in a parameter file, whose name generally (but not necessarily) has a ".param" extension. This file is updated during processing and can be read in on a subsequent run. Area (1) of the main window allows you to specify a parameter file, load parameters from the file, and save parameters to the file. If you specify a non-existent file and click "SAVE", a new file will be created. It is good practice to make a new parameter file for each dataset: start by loading a file from a similar dataset, or the prototype, change parameters as necessary, change the file name, and save it.
A number of "command files" are needed to run the various programs which are part of the system. These are kept in a standard location and copied to the current working directory before use. This is done automatically by the process script, but can also be done manually by clicking the "Get Cmd Files" button (2). You may need to do this if you have edited the command files and want to reset to the standard values, for instance. To edit command files before executing them, click "Edit Cmd File Before Execution". See command files section for much more about command files.
Area (3), and the "Directories:Images" field above it, specifies the image files to be processed. Files are sought for in the "Images" directory, and filenames are of the form "prefix_run_sequence.suffix", where "prefix" is given by the "Image Prefix" field, "run" by the "Run No." field, suffix by the "Filename suffix" field in the "Detector Parameters" window (see Detector types), and "sequence" runs from "Start Image No." to "End Image No.". Alternatively, the "Run No." field may be left blank and filenames are of the form "prefix_sequence.suffix". For indexing, and initial refinement, you will probably use only a subset of the complete set of frames (as specified in the indexing and refinement windows); "sequence" gives the range that will be integrated.
Area (4) contains a few basic parameters for this dataset. Other general parameters are shown, and can be changed, in the windows which you can pop up using the buttons at the top right (5). In particular, be sure to set the correct detector type and direction of spindle rotation in the "Machine Parameters" window. To change a parameter, type the new value in the appropriate text field. To save updated parameters to the current parameter file, click "SAVE". To save them to a new parameter file, enter a new name in "Parameter File" and click "SAVE".
To stop a process which has been started from the GUI, click "STOP". To exit from the GUI itself, click "CLOSE" (6).
Follow the flow chart across the middle of the GUI: indexing, refinement, integration, scaling, final output. The display and strategy steps are optional; an image display is produced automatically at various stages, and the strategy calculation is only useful when preliminary processing is done prior to data collection.