# Presentation: 313557

## Automar Data Reduction Protocol

-  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

## 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 cross 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

## 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**

## 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**

## Choose Header Items To Load

** ****Check the header items**
** ****By default, choose all the items**
** ****Users can uncheck any items**

## Modify Header Items in Setup

** ****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**
** **

## Open Frame to Display

** ****From Show Page, click Display **
** ****From File / Open image, browse and pick the first new frame**
** ****Load the frame**
**  **

## Frame Displayed

** ****Use Image Options to customize display features**
**  **

## 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**
**  **

## Update Beam Center in Setup

-  **Update beam center into Setup page with the measured beam center**

## Setup and Run Peak Search

-  **Use default setup or different criteria**
** ****Users may use different frame range to search peaks**
** ****Run Peak Search by click it**

## Result of Peak Search

-  **Users may redo the peak search for more satisfactory result by changing setup criteria**

## Text Result of Peak Search

-  **Users may click text in Show Page to monitor detailed text output **

## 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 click 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**

## Setup Update After marIndex

-  **Setup page will update all the parameters with indexed values**

## Run marPredict and Result

-  **Click Predict to run marPredict**
** ****Predicted reflection spots will be displayed on the display page**

## 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**

## Integration Output

-  **Integration will take several iterations with max number set by user in Integrate / Edit page**
** ****Integration will finish until cycles converge**
** ****Click Show Page / Text /Display to toggle between text output and frame display with updated prediction spots**

## Finish Integration

-  **End of integration job**

## Run Join to Create Scala Input

-  **Click Join / Edit**
** ****Choose “Use scala instead of marScale for scaling”**
** ****Click Join to run**

## Join Result

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

## Run Scala

-  **Click Scale / Edit**
** ****User may change any parameters for scala program**
** ****Click Scale to run scala**

## Scala Output

## Plot Output

-  **Click Plot button to choose scala output to plot**

## Pipeline Mode

** ****Check all the left Run check boxes to run all the programs consecutively**
** ****Click Run Selection to start pipeline**