D*TREK Data Reduction Protocol

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• 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 / 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

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Page 2

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

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Page 3

Select Image File in dtdisplay

• Pick the first frame in the data set

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Display Frame

• The first frame is displayed on the dtdisplay window

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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

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Select Image File in dtprocess

• Select the first image file

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Header Loaded

• After selecting 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
• Very carefully measure direct beam from dtdisplay window image
• Set Direct beam (px) to new values
• Click Write dtprocess.head to create new header file

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Page 8

Find Peaks

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

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Page 9

Find Result In dtdisplay

• Find result is displayed

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Page 10

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 fails, try to measure beam center again

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Page 11

Indexed Orientation Matrix

• Enter choice for different orientation matrix

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Page 12

Refinement

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

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Page 13

Create Predicted Reflections

• Click Predict
• Click Run Refinredict to run

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Display Prediction

• Predicted spots are displayed on dtdisplay window

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Integrate

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

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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

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Integrate Display

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

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Merge

• Click Merge
• Click Run merge to start

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Scale and Average

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

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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
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