Eppley Institute for Cancer Research

University of Nebraska Medical Center

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Project Settings Dialog Box

Where is it accessed?

The project settings dialog box is accessed with the project... command under the settings menu.

What does it do?

The project settings dialog box is actually a tabbed notebook object that allows the user to adjust project properties.  These changes are automatically mirrored in the .prj file.  The pages are grouped by function.  A detailed description of each tab follows.

General Tab


The General Tab allows the user to change settings about a project that are global.  Mainly it deals with file name templates and paths.  Additionally it provides a crystal id.  The crystal id is used in symmetry related reflection analysis to allow the user to group the results from multiple runs and multiple crystals.  BEAM-ish fills this information automatically when a new project is created.

Mosflm Tab


The Mosflm tab allows the user to adjust parameters that are used to start MOSFLM.

Halfslice Tab


The Halfslice tab allows the user to adjust parameters that are used to start HALFSLICE.  The most important are the last 4 parameters.  These need to be set to match the fine image set.  They are the Full Width parameter which should be equal to the closest odd number to the number of images in the fine image set.  The Start Image, which is typically 0 and the End Image which is typically 999.  The last parameter is the angular value for the image in the center of the set.  This value needs to be in degrees.  These settings are an artifact of how the program was originally built to run.  HALFSLICE can process images as they are acquired.  The is done by checking the "Enable Real-time Image Processing" button and then selecting a maximum amount of wait time between successive images in seconds.  On some systems the image header data is not properly stored.  On these systems "Header Angle Spoofing" can be enabled to allow BEAM-ish to work with these images.  The user needs to supply the image angle of image zero and the oscillation angle.  If the data set does not start on image zero, these values need to be enter for a hypothetical image starting at zero.

Peakstats Tab


The Peakstats tab allows the user to adjust the parameters that Peakstats uses when processing reflection profiles.  The most used setting deal with the averaging filter.  Check the "Use Averaging Filter" to apply an averaging filter.  The Edit box next to the check box allows the user to enter the width of the filter in images.  Values of 3 or 5 usually provide decent results.  Apply Dezinger and Print Profiles should always be checked unless some alternate use is needed.

Gaussians Tab


The Gaussians tab allows the user to select the default number of Gaussians that are fit when a reflection profile is switched to the needs refined mode.  This is useful when the user wishes to fit a large number of reflections at one time, which can be accomplished from the stat window.  When a reflection needs refined BEAM-ish will use a metric for the particular number of reflections or supply a simple default if none is available.  When using the LM method of fitting a metric should be defined.