Automar Data Reduction Protocol

Page 1



• 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
Next

Page2



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

PreviousNext
Page 3

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

PreviousNext
Page 4

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

PreviousNext
Page 5

Choose Header Items To Load



• Check the header items

• By default, choose all the items

• Users can uncheck any items

PreviousNext
Page 6



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

PreviousNext
Page 7

Open Frame to Display





• From Show Page, click Display

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

• Load the frame

PreviousNext
Page 8



Frame Displayed

• Use Image Options to customize display features

PreviousNext
Page 9



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

PreviousNext
Page 10

Update Beam Center in Setup

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



PreviousNext
Page 11



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




PreviousNext
Page 12



Result of Peak Search

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

PreviousNext
Page 13

Text Result of Peak Search

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

PreviousNext
Page 14



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

PreviousNext
Page 15

Setup Update After marIndex

• Setup page will update all the parameters with indexed values

PreviousNext
Page 16



Run marPredict and Result

• Click Predict to run marPredict

• Predicted reflection spots will be displayed on the display page

PreviousNext
Page 17



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

PreviousNext
Page 18



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

PreviousNext
Page 19



Finish Integration

• End of integration job

PreviousNext
Page 20



Run Join to Create Scala Input

• Click Join / Edit

• Choose "Use scala instead of marScale for scaling"

• Click Join to run

PreviousNext
Page 21



Join Result

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

PreviousNext
Page 22



Run Scala

• Click Scale / Edit

• User may change any parameter for scala program

• Click Scale to run scala

PreviousNext
Page 23



Scala Output

 

PreviousNext
Page 24



Plot Output

• Click Plot button to choose scala output to plot

PreviousNext
Page 25



Pipeline Mode

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

• Click Run Selection to start pipeline

PreviousBegin Over

Designed and maintained by the SER-CAT Webmaster.

We welcome your questions and comments. Send e-mail to: SER-CAT webmaster@anl.gov