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Name

automar - Graphical user interface for mar data processing programs (marPeaks, marIndex, marProcess, marPost, marScale and marStrategy).

Description

automar is a Motif-based graphical data processing of images collected with mar detectors (mar180/mar300/mar345/marccd/mar555) user interface for running programs marPeaks, marIndex, marStrategy, marProcess, marPost and marScale as well as the scaling program scala of the CCP4 suite. The program serves as a graphical input file editor. Emphasis was put on keeping manual input minimal and doing all essential parameter checks, so even unexperienced users can start right away to process data. The program features essentially only one window, from which all work is done.

Options

 image_file
Directly loads and displays the desired image file.
 directory
Uses the specified directory as working directory. The default is to use the current directory.

Mode of Operation

A typical data processing run consists of the following steps:

Technically, automar forks a new process when running either of the programs. Only one process can be run at one time.

When starting any of the programs, the contents of the "Setup" and/or "Edit" windows are written into files marPeaks.ctrl, marIndex.ctrl or marPredict.ctrl marStrategy.ctrl, marIntegrate.ctrl, mar2mtz.com or scale.com, respectively, and placed in the working directory. The ".ctrl" are control data input files. When running programs manually from a terminal window, the corresponding command would be for instance "marIndex marIndex.ctrl". The ".com" files are plain command files for programs mar2mtz and scala and can also be used manually.

automar saves current parameters into file automar.dat (and automar.bck). The directory location for this fil should be assigned by the environment variable AUTOMARDIR. If this variable is undefined it looks for directory MARLOGDIR/automar. If MARLOGDIR is undefined as well, the current directory will be used. At startup, the program may complain about missing file automar.dat. This message can be ignored.

Main Window

The main window consists of essentially 4 areas:

The menu bar provides options, extra tools and additional windows. The page selection area in the upper left hand side of the main window offers the choice of 6 "pages" with differing functions to be displayed in the flexible work area in the right hand side of the main window.

The program selection area allows for entering the most frequently used parameters (first and last image and maximum resolution). In this area one selects the program step(s) to run.

Menu Bar

The menu bar contains 4 items that can be selected by using the left mouse button or by pressing an accelerator key:
 File (Alt+f):
·
  • Open Image...: Pops up a file selection box for loading an image file.
  • Open Spots...: Pops up a file selection box for loading a spot file.
  • Save Image...: Pops up a window for saving an image file in several graphics formats.
  • Open Parameters...: Pops up a file selection box for loading a parameter file.
  • Save Parameters...: Pops up a window for saving current parameters.
  • (Preferences...)): Pops up a window for setting some program preferences.

    •  Options (Alt+o):
    ·
  • Read image header: read header of the image defined by "Data directory", "Image name root", "Image extension" (Setup window) and "First image" (Main Window).
  • Restore last set of parameters: reloads all parameters from before the last run of program marIndex and/or marIntegrate.
  • Restore default parameters: restores a set of (user definable) parameters from file $AUTOMARDIR/automar.defaults.
  • Clear Text: Remove all text from the text display area.
  • marView: Forks separate session of program marView
  • marTools: Forks separate session of program marTools.

    •  Image Options (Alt+i):
    ·
  • Resolution rings: Toggles resolution rings in image display window.
  • 3D plot: Toggles 3D plot in image display window.
  • Keep view: Toggles "keep view" in image display window. When loading new images, the same view (magnification, color scaling) will be maintained.
  • Keep colors: Toggles "keep colors" in image display window. When loading new images, the same color scaling will be maintained.
  • Fit screen (icon): Zoom out so that entire image fits screen.
  • Zoom in (icon): Increase magnification of image area by 2.
  • Zoom out (icon): Decrease magnification of image area by 2.
  • Integrate (icon): Integrates currently displayed image area (only for zoom factors >= 1).

    •  Show (Alt+s):
    Switches between pages (same functions as pressing buttons "Display", "Setup", "Text", "Index", "Strategy" and "Scale").

     Log files (Alt+l):
    Reads log files produced by selected programs and displays contents in the text area (or separate window).

     Help (Alt+h):
    Displays automar documentation in the desired HTML-viewer.

    Page Selection Area

    In the page selection area you can switch between several pages to be displayed in the right hand side area of the main window.
     Display (F1):
    Shows the image display window.
     Setup (F2):
    Sets the relevant parameters common to all program steps.
     Text (F3):
    Displays the terminal output (stdout) of programs when being run.
     Index (F4):
    Graphical visualization of results from program step marIndex
     Strategy (F5):
    Graphical visualization of results from program step marStrategy
     Scale (F6):
    Graphical visualization of results

    from program step Scale

    Program Selection Area

    In the program selection area you can set the most frequently modified parameters ("First image", "Last image" and "Max. resolution"). The main function, however, is to start individual program steps by pressing any of the blue buttons or a sequence of program steps by (de-)selecting the "Run" buttons and pressing the "Run Selection" button. Program parameters specific to certain program steps can be edited by pressing the "Edit" button of the left hand side of the corresponding program step button. If no step specific parameters exist (marIndex, mar2mtz), the "Setup" window is displayed.

    Setup Window

    To obtain the Setup window, select Setup in the page selection area or type: F2.

    The window is divided into 5 logical units for entering parameters.

     Crystal parameters:
  • Spacegroup.
  • Unit cell axes and angles.
  • Orientation x,y,z in degrees.
  • Spot size in mm.
  • Mosaic spread in degrees.

    • All Laue groups are implemented in program denzo to take care of all possible crystal symmetries, but only a selection of particular space groups may be input. In case of doubt you should choose the Laue group only. The worst thing that can happen is that there systematic absences from additional screw axes are not removed from the reflection list.

    By default, the unit cell parameters will automatically be updated when running marIntegrate. Note, that the updated parameters will correspond to the refined parameters from the first image only!

     Goniometer parameters:
  • Distance.
  • Starting PHI position.
  • Oscillation range per image.
  • Two theta, chi and omaga.

    •  Beam parameters:
    ·
  • Wavelength.
    • ·
  • Beam divergence (horizontal and vertical).

    •  Detector parameters:
    ·
  • Beam center.
    • ·
  • Pixel size.
  • Radial and angular scanner offset.
  • Tilt, twist and turn.

    • Index Window

    To obtain the Index window, select Index in the page selection area or type: F4.

    Strategy Window

    To obtain the Strategy window, select Strategy in the page selection area or type: F5.

    Here you can plot the relevant contents of the output file from program marStrategy. The file Working_directory/AUTOMAR.strategy is processed. The big wheel is a representation of the scanner’s PHI axis. The PHI range that has been used when running marStrategy is displayed as violet spiral the start of the spiral being the "Starting PHI" and the end of the spiral being the "Ending PHI". The slices inbetween the "Starting PHI" as given in the input field of the Plot window and the "Starting PHI + Total PHI" are orange. Note, that the completeness in the desired range can be printed only if it has been determined previously in marStrategy. If the desired areas and precalculated do not overlap at all, the program will complain. The cumulative completenesses are printed in red letters outside the circle. On the bottom, the 8 top strategies are displayed with corresponding completeness and PHI range.

    Scale Window

    To obtain the Scale window, select Scale in the page selection area or type: F6.

    Here you can plot the relevant contents of the output file from program scala (Rsym, etc.).

    Input Files

    $AUTOMARDIR/automar.dat
    Always contains the latest set of parameters. Each time one input field changes, this file is being updated.

    Output Files

    The program produces the following output file:
    $AUTOMARDIR/automar.dat
    Latest set of program parameters.
    $AUTOMARDIR/automar.bck
    Before running program marIndex and/or marIntegrate, the current parameters are being saved to this file. This is because you may choose to automatically overwrite some parameters like distance and orientation during refinement. At the end of the job, it may turn out that the refined values are nonsense, so you will want to restore the latest set of parameters from this file.
    Working_directory/AUTOMAR.peaks
    Output log file of marPeaks.
    Working_directory/AUTOMAR.index
    Output log file of auto-indexing.
    Working_directory/AUTOMAR.predict
    Output log file of marPredict.
    Working_directory/AUTOMAR.strategy
    Output log file of marStrategy.
    Working_directory/AUTOMAR.integrate
    Output log file of marIntegrate.
    Working_directory/AUTOMAR.scale
    Output log file of scala.

    Command Files

    When running programs, automar produces the following command files:
    Working_directory/marPeaks.ctrl
    Data input file for program marPeaks
    Working_directory/marIndex.ctrl
    Data input file for program marIndex
    Working_directory/marPredict.ctrl
    Data input file for program marPredict
    Working_directory/marStrategy.ctrl
    Data input file for program marStrategy
    Working_directory/marIntegrate.ctrl
    Data input file for program marIntegrate
    Working_directory/mar2mtz.com
    Command file for running programs mar2mtz and sortmtz.
    Working_directory/scale.com
    Command file for running program scala.

    See Also

    marView, marTools, marpeaks, marstrategy

    Author

    Claudio Klein, marXperts GmbH, Norderstedt, Germany

    Copyright

    © Copyright 2014 marXperts GmbH, Norderstedt, Germany

    Address

    marXperts GmbHPhone: +49 - (40) - 529 884-0
    Werkstr. 3 FAX: +49 - (40) - 529 884-20
    D-22844 Norderstedt - GERMANYinfo@marXperts.com
    www.marXperts.com

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