Automar Data Reduction Protocol

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• Reformat frames from Omega scan axis to Phi axis

• Make local process directory for Automar output

• Start Automar GUI and follow program flow chart

• Load frame header and modify beam center, distance

• Run Automar / marIndex

• Run Automar / marPredict

• Run Automar / marProcess to start integration

• Run Automar / Join to create .mtz for CCP4 scala

• Run Automar / Scale to run CCP4 scala

• Keep final output log file: AUTOMAR.automar.scala

• Keep final output mtz file: scala.automar.mtz
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Reformat Frames From Omega to Phi

•Reformat frames from Omega scan axis to Phi

• Reformat is very time consuming

• New frames should be saved locally instead of across network disks

• Type "reformat_frames" to get help

• Example:

$ reformat_frames -p lyso.####   phi/lyso.####   1  180

• -p will force Omega to Phi

• lyso.#### are original data frames

• phi is the new frame directory created

• phi/lyso.#### are the new data frames

• 1   180 is the frame range from 1 to 180

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Start Automar Program




•Change to Automar process local directory

•Start Automar: $ automar

•Session will be saved in file automar.mix in local directory

•Session file could be used for future data reprocessing

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Load Frame Header in Setup Page





• From Show Page, go to Setup

• Working directory will be automatically set to local dir

• Browse the image directory

• Select the first frame from dir

• Click Load Image Header

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Choose Header Items To Load



• Check the header items

• By default, choose all the items

• Users can uncheck any items

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Modify Header Items in Set up



  • • For mar225 detector,
    Change the distance value as:
    new = header value – 7.5
    example as shown:
    new = 100 – 7.5 = 92.5 mm

    Change the beam center by next step

  • • For mar165 detector, only change beam center

  • • For both detectors, change Polarization to 0.95 as synchrotron

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Open Frame to Display





• From Show Page, click Display

• From File / Open image, browse and pick the first new frame

• Load the frame

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Frame Displayed

• Use Image Options to customize display features

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Measure Beam Center

• Zoom in the beam center by hold / drag right mouse button

• Measure beam center with middle mouse button

• The beam center of the cross is displayed in the left bottom corner

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Update Beam Center in Setup

• Update beam center into Setup page with the measured beam center



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Setup and Run Peak Search

• Use default setup or different criteria

• Users may use different frame range to search peaks

• Run Peak Search by clicking it




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Result of Peak Search

• Users may redo the peak search for more satisfactory results by changing setup criteria

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Text Result of Peak Search

• Users may click text in Show Page to monitor detailed text output

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Run marIndex and Result

• Click Index to start marIndex

• The correct indexed lattice and cell will be picked by program

• User may change the indexed lattice and cell by clicking the line, then rerun the index

•User may put in known cell and space group in Setup page to force program to index to known result

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Setup Update After marIndex

• Setup page will update all the parameters with indexed values

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Run marPredict and Result

• Click Predict to run marPredict

• Predicted reflection spots will be displayed on the display page

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Run marProcess and Integration

• Click Integrate / Edit

• Uncheck the beam divergence for synchrotron source

• Change Print output from compact to extended

• Change trusted pixel intensity to known detector max linear pixel value

• Click Integrate to start

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Integration Output

• Integration will take several iterations with the max number set by user in Integrate / Edit page

• Integration will continue until cycles converge

• Click Show Page / Text /Display to toggle between text output and frame display with updated prediction spots

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Finish Integration

• End of integration job

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Run Join to Create Scala Input

• Click Join / Edit

• Choose "Use scala instead of marScale for scaling"

• Click Join to run

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Join Result

• User may change crystal space group to higher symmetry by changing Setup page parameters after running Join for scala

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Run Scala

• Click Scale / Edit

• User may change any parameter for scala program

• Click Scale to run scala

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Scala Output

 

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Plot Output

• Click Plot button to choose scala output to plot

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Pipeline Mode

• To run all the programs consecutively, select all the check boxes under Run.

• Click Run Selection to start pipeline

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