Eppley Institute for Cancer Research
University of Nebraska Medical Center
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Eppley Institute for Cancer Research |
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University of Nebraska Medical Center |
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Processing data is carried out in three steps a fourth optional step is fitting on Gaussians to profiles. The three main steps are represented by the buttons on the left side of the BEAM-ish main window. This page will describe each step and highlight important things that should be done.
Prerequisites
Have coarse diffraction images.
What are the goals?
Determine the orientation matrix.
Select the locations where reflections will be profiled.
Do a simple integration to generate an MTZ file which will contain all of the above data.
Things to do
On the BEAM-ish settings dialog box make sure that the executable for MOSFLM is correctly entered.
On the MOSFLM tab of the project settings dialog box make sure the following information is correct before pressing the mosflm button.
The most important boxes are the Beam Centers for the X and Y locations. These coordinates must be entered in mm as they would be in MOSFLM. This may require a calculation by the user.
Make sure the wavelength Lambda is correct.
Check that the correct crystal to detector distance is entered.
Finally, make sure that the Image to Open is set to one of the coarse images.
Prerequisites
Have a fine phi data set that is continuous between the start and end indexes.
Have an MTZ file generated from MOSFLM.
What are the goals?
Generate profile for selected reflections.
Things to do
On the BEAM-ish settings dialog box make sure that the executable for HALFSLICE is correctly entered.
On the HALFSLICE tab of the project settings dialog box make sure the following information is correct before pressing the HALFSLICE button.
Use the browse button to select the MTZ file that was created with MOSFLM. The HALFSLICE button will not become enable unless this file exists.
The most important thing is that the correct value for the Mid Angle. This can be found in the image header which BEAM-ish writes to the terminal when an image is opened. If this value is not set properly then HALFSLICE will not properly generate the profiles for the reflections.
Be sure to set the value for Full Width be set to the closest odd number of images in the data set (usually 999 but may be less).
Make sure the start and end image indexes are correct (usually 000 to 999).
Prerequisites
HALFSLICE must have completed and written files successfully.
What are the goals?
Remove zingers from the profiles.
Smooth out noise with an averaging filter.
Identify the peak locations and properties within the profile.
Determine profile offsets in the DAT2 file to improve lookup time in BEAM-ish.
Report the statistics back to files for use by BEAM-ish.
Things to do
On the BEAM-ish settings dialog box make sure that the executable for PEAKSTATS is correctly entered.
On the PEAKSTATS tab of the project settings dialog box make sure the following information is correct before pressing the PEAKSTATS button. The PEAKSTATS button will only be enabled after HALFSLICE has successfully completed.
Make sure that the values for Sigma X, Sigma Y and Sigma Z are filled in correctly. The values must be calculated by the beam line scientist at the synchrotron and should be the same for several shifts of beam time. These value are critical for calculating the corrected mosaicity.
Setup the averaging filter parameters as desired. For microgravity crystals it may not be necessary to even use an averaging filter. For earth grown crystals a filter width of 3 should improve calculations.
The apply dezinger and print profile options should always be checked.
Prerequisites
PEAKSTATS must have completed and written files successfully for the Fit Manager to be enabled.
What are the goals?
Fit one or more Gaussians to a profile.
Things to do
This topic has it own page located at Fitting Gaussians to Profiles.
