# Presentation: 897390

## D*TREK Data Reduction Protocol

-  Make local process directory for d*TREK output
-  Start d*TREK GUI and follow program flow chart
-  Load frame from data directory
-  Load frame header and modify beam center, distance
-  Modify Setup parameters
-  Run dtprocess / Find
-  Run dtprocess / Index
-  Run dtprocess / Refine
-  Run dtprocess / Predict
-  Run dtprocess / Integrate
-  Run dtprocess / Merge
-  Run dtprocess / Scale / Average
-  Keep final output .log file: dtscaleaverage.log
-  Keep final .ref file: dtscale.ref
-  d*TREK final .ref could be converted into .mtz in CCP4

## Start d*TREK Program

** ****Change to d*TREK process local directory**
** ****Start d*TREK: $ dtprocess**
** ****Several windows will be opened**
** ****Browse and pick the first image if it is the first time to process data in the local directory**
** ****Browse and pick the appropriate .head file if data has been processed before**

## Select Image File in dtdisplay

** ****Pick the first frame in the data set**

## Display Frame

** ****The first frame is displayed on the dtdisplay window**

## Select Header File or Image File

** ****Go to dtprocess window**
** ****Browse and pick the .head file, such as dtprocess.head**
** ****If there are not .head files in the directory, pick the first image file instead**

## Select Image File in dtprocess

** ****Select the first image file**

## Header Loaded

** ****After select header file or image file, header information is loaded**
** ****Set Flow chart mode**
** ****Set Spatial distortion type to Simple**
** ****Set Mask / Non-uniformity type to None**
** ****Set Det distance (mm) to new value:**
**        ****new = old – 7.5**
**   ****example:**
**        ****new = 100 – 7.5 = 92.5**
** ****Measure direct beam from dtdisplay window image displayed very carefully**
** ****Set Direct beam (px) to new values**
** ****Click Write dtprocess.head to create new header file**

## Find Peaks

** ****Click Find**
** ****Use default or set new parameters**
** ****Click Run find to start Find**

## Find Result In dtdisplay

** ****Find result is displayed **

## Index

** ****Click Index to start run**
** ****From Input, <Enter> or <cr> will select the indexed lattice**
** ****Index routine is very sensitive to the beam center and detector distance**
** ****If autoindex failed, try to measure beam center again**

## Indexed Orientation Matrix

** ****Enter choice for different orientation matrix**

## Refinement

** ****Click Refine**
** ****Click Run refine to start refinement**
** ****User may choose different Macros for refinement**

## Create Predicted Reflections

** ****Click Predict**
** ****Click Run predict to run**

## Display Prediction

** ****Predicted spots are displayed on dtdisplay window**

## Integrate

** ****Click Integrate**
** ****Use default or new parameters **
** ****Click Run integrate to run**

## Integrate Output

** ****Integrate output will be displayed in dtprocess window**
** ****Log file will be created as highlighted file name**
** ****Current header file is highlighted and may be used for future reprocess**

## Integrate Display

** ****During integrate, each image and predicted reflection spots will be displayed in dtdisplay window**

## Merge

** ****Click Merge**
** ****Click Run merge to start**

## Scale and Average

** ****Click Scale / Average**
** ****Use default or new parameters to do the scaling**
** ****Batch + 4****th**** 3D Abscor method is recommended**
** ****Reject percentage should be manually changed by user **
** ****Click Run scale to start**

## Scale Output

** ****Scaling result is displayed in dtprocess window**
** ****Output log is written into dtscaleaverage.log**
** ****Output reflection is written into dtscale.ref**
** ****User may change Flow chart mode to run all the jobs consecutively**