6. Enter the correct ROTATION_AXIS values according to the
direction of rotation and predetermined detector geometry,
which differs by instrument.
7. Based on a visual inspection of the stack of diffraction images in
Adxv, pinpoint the specific range of frames which incorporates
the highest quality data to be used for indexing. Set SPOT_RANGE as this set of frames. Avoid frames with visible defects
such as polycrystalline reflections or overly elongated, ellipsoidal spots. DATA_RANGE specifies the range of images used
for integration and can include all the frames specified in
SPOT_RANGE and more.
8. Run XDS. If no errors occur, proceed to step 9. If errors
appear, see Note 17.
9. The stringency of IDXREF may result in the frequent appearance of errors, prematurely halting further processing. If confidence in indexing is high, these halts can be circumvented by
modifying the JOB settings in the XDS.INP input file as suggested by the error output and rerunning XDS (see Note 18).
10. Optimize the indexing solution by adjusting parameters such
as the set of frames used for indexing and integration, the
minimum number of pixels in a peak, the thresholds for background and peak pixel selection, and the mosaicity model (see
Note 19).
11. Run XSCALE on the optimized indexing solution.
12. Repeat steps 1–10 for each movie collected.
3.5 Dataset Merging
1. To merge datasets, create a new XSCALE.INP input file.
2. Specify the respective file paths of each desired XDS_ASCII.
HKL file using INPUT_FILE (see Note 20).
3. Run XSCALE. Analyze the statistics of the merged solution in
XSCALE.LP (see Note 21) (Fig. 4a).
4. Once a satisfactory merge is successfully implemented, open
XDSCONV.INP and set the output type and file extension to
SHELX and “.hkl,” respectively.
5. Run XDSCONV to convert the scaled reflection file generated
by XSCALE (with an “.ahkl” extension) to “.hkl” format. This
renders it readable by SHELX.
6. Alternatively, open XDSCONV.INP and set the output type
and file extension to CCP4_I+F and “.ascii,” respectively. Run
XDSCONV. XDSCONV may prompt the user for additional
CCP4 commands to be executed, generating a binary list of
reflections with the extension “.mtz”.
7. Visualize the “.mtz” file (Fig. 4b) with viewHKL and search for
systematic absences to aid in space group determination.
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Chih-Te Zee et al.
direction of rotation and predetermined detector geometry,
which differs by instrument.
7. Based on a visual inspection of the stack of diffraction images in
Adxv, pinpoint the specific range of frames which incorporates
the highest quality data to be used for indexing. Set SPOT_RANGE as this set of frames. Avoid frames with visible defects
such as polycrystalline reflections or overly elongated, ellipsoidal spots. DATA_RANGE specifies the range of images used
for integration and can include all the frames specified in
SPOT_RANGE and more.
8. Run XDS. If no errors occur, proceed to step 9. If errors
appear, see Note 17.
9. The stringency of IDXREF may result in the frequent appearance of errors, prematurely halting further processing. If confidence in indexing is high, these halts can be circumvented by
modifying the JOB settings in the XDS.INP input file as suggested by the error output and rerunning XDS (see Note 18).
10. Optimize the indexing solution by adjusting parameters such
as the set of frames used for indexing and integration, the
minimum number of pixels in a peak, the thresholds for background and peak pixel selection, and the mosaicity model (see
Note 19).
11. Run XSCALE on the optimized indexing solution.
12. Repeat steps 1–10 for each movie collected.
3.5 Dataset Merging
1. To merge datasets, create a new XSCALE.INP input file.
2. Specify the respective file paths of each desired XDS_ASCII.
HKL file using INPUT_FILE (see Note 20).
3. Run XSCALE. Analyze the statistics of the merged solution in
XSCALE.LP (see Note 21) (Fig. 4a).
4. Once a satisfactory merge is successfully implemented, open
XDSCONV.INP and set the output type and file extension to
SHELX and “.hkl,” respectively.
5. Run XDSCONV to convert the scaled reflection file generated
by XSCALE (with an “.ahkl” extension) to “.hkl” format. This
renders it readable by SHELX.
6. Alternatively, open XDSCONV.INP and set the output type
and file extension to CCP4_I+F and “.ascii,” respectively. Run
XDSCONV. XDSCONV may prompt the user for additional
CCP4 commands to be executed, generating a binary list of
reflections with the extension “.mtz”.
7. Visualize the “.mtz” file (Fig. 4b) with viewHKL and search for
systematic absences to aid in space group determination.
338
Chih-Te Zee et al.