D*TREK Data Reduction Protocol

Page 1

• 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

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

Page 3

Select Image File in dtdisplay

• Pick the first frame in the data set

Page 4

Display Frame

• The first frame is displayed on the dtdisplay window

Page 5

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

Page 6

Select Image File in dtprocess

• Select the first image file

Page 7

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

Page 8

Find Peaks

• Click Find

• Use default or set new parameters

•Click "Run find" to start Find

Page 9

Find Result In dtdisplay

• Find result is displayed

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

Page 11

Indexed Orientation Matrix

• Enter choice for different orientation matrix

Page 12

Refinement

• Click Refine

• Click Run refine to start refinement

• User may choose different Macros for refinement

Page 13

Create Predicted Reflections

• Click Predict

• Click Run Refinredict to run

Page 14

Display Prediction

• Predicted spots are displayed on dtdisplay window

Page 15

Integrate

• Click Integrate

• Use default or new parameters

• Click Run integrate to run

Page 16

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

Page 17

Integrate Display

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

Page 18

Merge

• Click Merge

• Click Run merge to start

Page 19

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

Page 20

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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