DIALS processing of Mac1 data for diffuse scattering¶
The data were collected at ALS 8.3.1 on 2025-06-24.
Processing performed on the CLASSE compute farm (CHESS).
rsync'd data from ALS to CHESS: /nfs/chess/scratch/user/spm82/als_20250624
Note: the scratch directory is not backed up to tape. Consider moving to a backed-up location (raw? aux? user?)
Available datasets¶
16:27:05.8605588050 ./Plate1/H9_1_00001.cbf 16:32:18.6024715990 ./Plate1/H9_2_00001.cbf 16:35:42.2674603150 ./Plate1/H9_3_00001.cbf 16:38:35.8197459250 ./Plate1/H9_air_4_00001.cbf 17:09:11.9057517230 ./Plate1_H6/H6_5_00001.cbf 17:14:26.3996981060 ./Plate1_H6/H6_6_00001.cbf 17:17:55.5166686470 ./Plate1_H6/H6_air_7_00001.cbf 17:27:45.4949348410 ./Plate1_H8/H8_8_00001.cbf 17:31:20.1548458890 ./Plate1_H8/H8_9_00001.cbf 17:33:52.0983664420 ./Plate1_H8/H8_air_10_00001.cbf 17:49:29.4002659240 ./Plate1_G8/G8_1_00001.cbf 17:54:10.9235677980 ./Plate1_G8/G8_2_00001.cbf 17:57:35.1366085830 ./Plate1_G8/G8_air_3_00001.cbf 17:58:59.9807941110 ./Plate1_G8/G8_air_4_00001.cbf 18:11:34.0685697520 ./lyso/lyso_1_00001.cbf 18:14:47.4877172260 ./lyso/lyso_air_2_00001.cbf
Notes from visual inspection of the images in adxv
H9- first dataset, crystal rotated out of the beam (centered on gunk, not crystal)
- second dataset, way too much exposure time
- third dataset?
H6- first dataset, looks OK by eye (not too much damage)
- second dataset, looks OK by eye (not too much damage)
H8- first dataset, looks OK by eye (not too much damage)
- second dataset, looks to be lower resolution
G8- first dataset, looks OK by eye (not too much damage)
- second dataset, longer detector distance (250 mm), looks OK by eye (not too much damage)
H6_5 / H6_air_7¶
DIALS (first 90 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624
mkdir -p macrodomain_H6/dials
cd macrodomain_H6/dials
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H6/H6_5_00001.cbf:1:900
DIALS (first 180 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624
mkdir -p macrodomain_H6/dials_180
cd macrodomain_H6/dials_180
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H6/H6_5_00001.cbf:1:1800
Observations:
- Damage seems to be tolerable for the first 90 degrees (B-decay ~2 ang^2).
- The 180 degree dataset has much worse R-factors (B-decay by > 4 ang^2)
XIA2 summary (first 90 degrees of data):
Project: AUTOMATIC Crystal: DEFAULT Sequence length: 0 Wavelength: NATIVE (0.88553) Sweep: SWEEP1 Files /nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H6/H6_5_#####.cbf Images: 1 to 900 Beam 213.97 212.71 => 214.19 212.36 Distance 175.40 => 174.22 Date: Tue Jun 24 14:09:11 2025 For AUTOMATIC/DEFAULT/NATIVE: High resolution limit 1.06 2.88 1.06 Low resolution limit 63.01 63.12 1.08 Completeness 98.4 99.7 99.1 Multiplicity 3.3 3.3 3.2 I/sigma 17.3 86.5 0.8 Rmerge(I+/-) 0.033 0.020 1.334 CC half 0.998 0.997 0.318 Anomalous completeness 82.8 93.7 79.3 Anomalous multiplicity 1.8 1.8 1.8 Cell: 89.108 89.108 39.928 90.000 90.000 90.000 Spacegroup: P 41
H8_8¶
DIALS (first 90 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624
mkdir -p macrodomain_H8/dials_90
cd macrodomain_H8/dials_90
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H8/H8_8_00001.cbf:1:900
DIALS (first 180 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624
mkdir -p macrodomain_H8/dials_180
cd macrodomain_H8/dials_180
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H8/H8_8_00001.cbf:1:1800
DIALS (all 360 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624
mkdir -p macrodomain_H8/dials_360
cd macrodomain_H8/dials_360
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H8/H8_8_00001.cbf:1:3600
Observations:
- The first 90 degrees has low completeness (missing wedge).
- First 180 degrees is better, and radiation damage is minimal.
- All 360 degrees looks fine. There is a jump in R-factor around frame 3000 or so, might be worth investigating
XIA2 summary (all 360 degrees of data):
Project: AUTOMATIC Crystal: DEFAULT Sequence length: 0 Wavelength: NATIVE (0.88553) Sweep: SWEEP1 Files /nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_H8/H8_8_#####.cbf Images: 1 to 3600 Beam 213.94 212.71 => 214.19 212.37 Distance 175.40 => 174.40 Date: Tue Jun 24 14:27:45 2025 For AUTOMATIC/DEFAULT/NATIVE: High resolution limit 1.06 2.87 1.06 Low resolution limit 89.05 89.36 1.08 Completeness 99.7 100.0 94.7 Multiplicity 13.0 13.3 12.9 I/sigma 11.6 74.9 0.4 Rmerge(I+/-) 0.080 0.035 3.152 CC half 1.000 0.999 0.355 Anomalous completeness 99.7 100.0 94.8 Anomalous multiplicity 6.6 7.0 6.5 Cell: 89.045 89.045 39.818 90.000 90.000 90.000 Spacegroup: P 41
G8_1 / G8_air_4¶
DIALS (first 90 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624/
mkdir -p macrodomain_G8/dials
cd macrodomain_G8/dials
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_G8/G8_1_00001.cbf:1:900
DIALS (all 360 degrees)
cd /nfs/chess/user/spm82/mdx/als_20250624/
mkdir -p macrodomain_G8/dials_360
cd macrodomain_G8/dials_360
xia2 image=/nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_G8/G8_1_00001.cbf:1:3600
XIA2 summary (all 360 degrees of data):
Project: AUTOMATIC Crystal: DEFAULT Sequence length: 0 Wavelength: NATIVE (0.88553) Sweep: SWEEP1 Files /nfs/chess/scratch/user/spm82/als_20250624/macro/6-23-25/Plate1_G8/G8_1_#####.cbf Images: 1 to 3600 Beam 213.94 212.71 => 214.17 212.37 Distance 175.40 => 174.36 Date: Tue Jun 24 14:49:29 2025 For AUTOMATIC/DEFAULT/NATIVE: High resolution limit 1.08 2.93 1.08 Low resolution limit 63.09 63.20 1.10 Completeness 100.0 100.0 100.0 Multiplicity 13.1 13.3 12.7 I/sigma 9.6 52.7 0.5 Rmerge(I+/-) 0.106 0.050 2.534 CC half 0.999 0.999 0.370 Anomalous completeness 100.0 100.0 100.0 Anomalous multiplicity 6.7 7.0 6.4 Cell: 89.219 89.219 40.178 90.000 90.000 90.000 Spacegroup: P 41