2025-10-15 @ ALS 8.3.1
Date Created: 2025-10-15
Tags: ALS 831, Mac1, Huwe1
Kara's and Violla's first try at collecting diffuse data
Overall Goals
- (Try to) Optimize diffuse collection at 8.3.1
- Mac1 and Huwe1 collection, looping in the humidity box with sleeves
- Mac1 and Huwe1 collection, looping under the watershed with sleeves
- Take background at a few different positions
- Collect data at different temperatures with oil and/or sleeves
Participants
Kara and Violla
Data
Root directory at ALS: /data/mcfuser/ucsf/fraser/15Oct2025/diffuse
Beamline Settings
Converting the beamline from conventional cryo setup to room temperature, diffuse setup:
cryojet.com off
cryojet.com move out
wave.com 14000
tuneup.com
dcsmotor.com transmission 0.01
divergence.com 0.9 (had to play around here to get dose around 1000 Gy/s)
diode.com in
shutter.com open
flux.com
Day 1 Parameters
| Parameter | Value | Notes |
|---|---|---|
| X-ray energy | 14000 eV @ 0.014 % bandwidth | |
| Beam size | 100 µm x 100 µm, Gaussian profile | |
| Flux | 1.865 x 10¹⁰ ph/s | 1052 Gy/s |
| Beamstop | standard 8.3.1 | |
| Data collection software | Blu-Ice | |
| Temperature control | 297K | cold stream was removed but kept on with 297K setpoint |
Samples
| Name | Sample | Well composition | Drop composition | Notes |
|---|---|---|---|---|
| Mac1 | SARS CoV2 NSP3 macrodomain and seed stock. 40 mg/mL Mac1 in 150 mM NaCl, 20 mM Tris pH 8, 5% glycerol | 34% (w/vol) PEG 3000 + 100 mM CHES (pH 9.5) | 200 nL protein solution + 100 nL well solution + 100 nL seeds | Tray 1349 Set up by Galen |
| Huwe1 | 88 mg/mL | NaCl 2-3.5M NaOac 50-200mM pH 4.84 | 200 nL protein solution + 200 nL well solution | Tray Number 1182 and 1183, at 4C |
Data Collection
Watershed, Mac1 Crystal 1
Loop location: Watershed
Loop size: 200 µm
Relative Humidity: 90.6% with max flowrate, close to tray
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_1 | 0 | 720 | 0.1 | 7200 | 0.1 | 200 | did not sleeve directly under watershed, still getting the hang, had shutter closed for first part, diffraction is a little weak - killed around 540 deg |
| mac1_1_bg_1 | 0 | 720 | 1 | 720 | 1 | 200 | went 200 µm away to fully clear the loop, accidentally overrode the beginning |
| mac1_1_bg_real | 0 | 720 | 1 | 720 | 1 | 200 | went 100µm down to be slightly below the loop |
Takeaway: practice run, try to do better job looping under watershed and move the detector back a bit
Day 2
tuneup.com
dcscan.com transmission 0.01
divergence.com 0.9
diode.com in
shutter.com on
flux.com
Day 2 Parameters
| Parameter | Value | Notes |
|---|---|---|
| X-ray energy | 14000 eV @ 0.014 % bandwidth | |
| Beam size | 100 µm x 100 µm, Gaussian profile | |
| Flux | 1.945 x 10¹⁰ ph/s | 1097 Gy/s |
| Beamstop | standard 8.3.1 | |
| Data collection software | Blu-Ice | |
| Temperature control | none | cold stream was removed and turned off |
Watershed, Mac1 Crystal 2
Loop location: Watershed
Loop size: 150 µm
Relative Humidity: 91.1%, 15 flowrate
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_2 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | well E3, plate 1349, diffraction quality varied throughout scan, maybe crystal died at certain points |
| mac1_2_bg_1 | 0 | 720 | 1 | 720 | 1 | 300 | started at same starting phi as crystal, 250 µm away, no height change |
| mac1_2_bg_2 | 0 | 720 | 1 | 720 | 1 | 300 | started at same phi as crystal, went 100 µm down |
Watershed, Mac1 Crystal 3
Loop location: Watershed
Loop size: 200 µm
Relative Humidity: 87.5%, 15 flowrate
Notes: Turned beamline feedback off as it tries to change the transmission. Redid tuneup and dropped divergence down. Flux: 1.9 x 10¹⁰, 1073 Gy/s with feedback off.
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_4 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | well E3, plate 1349, weak diffraction |
| mac1_4_2 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | re-centered, weak diffraction, abort |
Watershed, Mac1 Crystal 5
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_5 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | still weak diffraction |
| mac1_5_2 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | increased divergence to 0.2, flux is at 3.7 x 10¹⁰, dose is 2089 Gy/s, still bad diffraction |
Raster: nothing
Humidity Box, Mac1 Crystal 6
Relative humidity: 97.5%
Dose rate: 1021 Gy/s, divergence 1.2, Se in (attenuation)
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_6_2 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | everything looks good |
| mac1_6_bg_1 | 0 | 720 | 1 | 720 | 1 | 300 | went 200 µm away, transmission may not be correct |
| mac1_6_bg_2 | 0 | 720 | 1 | 720 | 1 | 300 | went 100µm down, transmission may not be correct |
| mac1_6_bg_3 | 0 | 720 | 1 | 720 | 1 | 300 | stayed in same spot, put transmission in blu-ice at 1.25% and collect |
JAMES INPUT:
# move sample out of the beam
sample.com 0 0 -1
diode.com in
shutter.com open
divergence.com 2 0.35
flux.com
# note the predicted dose rate in Gy/s
dcsmotor.com transmission 0.0003
flux.com
# note dose rate again. Adjust commanded transmission until dose rate is > 1000 Gy/s, but close-ish to it
flux.com
divergence.com 1.2
flux.com
# adjust divergence to get as close as you like to 1000 Gy/s
# now go to BLU-ICE and hit "update". This will load the actual transmittance into the run info
flux.com
shutter.com close
diode.com out
# put sample back in beam
sample.com 0 0 1
Takeaway: make sure you are running new adxv with small spots and weak data turned on. ALSO do NOT hit update on Blu-Ice, just enter the transmission value
Humidity Box, Mac1 Crystal 7
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_7 | 0 | 720 | 0.1 | 7200 | 0.1 | 300 | gorgeous, first collection where we actually know what the beamline is doing, possibly some damage by the end, took a post exposure picture |
| mac1_7_bg_1 | 0 | 720 | 1 | 720 | 1 | 300 | went 250 µm away |
| mac1_7_bg_2 | 0 | 720 | 1 | 720 | 1 | 300 | went 100 µm down |
Humidity Box, Mac1 Crystal 8
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_8 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | diffraction still looks good, crystal lifetime seems better as well |
| mac1_8_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 200 µm away |
| mac1_8_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100 µm down |
** For crystal 8 and forward, message from ALS that beam is longitudinally unstable**
Humidity Box, Mac1 Crystal 9
Check everything - all good!!
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_9 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | all good |
| mac1_9_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 250 µm away |
| mac1_9_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100 µm down |
Humidity Box, Huwe1 Crystal 1
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_1 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | diffraction is nice but not as strong as Mac1, maybe increase exposure time again |
** BEAM DOWN :(**
Beam back, but lower current. Did tune up and adjusted divergence to get higher dose rate with lower current.
Humidity Box, Huwe1 Crystal 2
Loop size: 300 µm and still probably too small
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_2 | 0 | 720 | 0.1 | 7200 | 0.1 | 350 | diffraction to 1.9, def damaged, lost some frames in the middle to accidentally closing the shutter |
| huwe1_2_bg_1 | 0 | 720 | 1 | 720 | 1 | 350 | went 300 µm away |
| huwe1_2_bg_2 | 0 | 720 | 1 | 720 | 1 | 350 | went 100 µm down |
Humidity Box, Huwe1 Crystal 3
Loop size: 300 µm and still probably too small
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_3 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | crystal lifetime seems better and crystal sat better in the loop |
| huwe1_3_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | 300 µm away |
| huwe1_3_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | 100 µm down |
** Current started increasing slowly during bg 1**
Humidity Box, Huwe1 Crystal 4
Loop size: 300 µm and still probably too small
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_4 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | very nice diffraction |
| huwe1_4_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | 300 µm away |
| huwe1_4_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | 100 µm down |
Humidity Box, Huwe1 Crystal 5
Loop size: 300 µm and still probably too small
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_5 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | very nice diffraction |
| huwe1_5_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | 250 µm away |
| huwe1_5_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | 100 µm down |
Day 3
Tuneup done
Transmission check: 1.9 x 10¹⁰ ph/s or 1075 Gy/s
Beam current: stable at 500 mA
Humidity Box, Mac1 Crystal 10
Source: Take from hanging drop tray
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_10 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | looks good but some lifetime issues |
| mac1_10_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 300 µm away |
| mac1_10_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100 µm down |
Humidity Box, Mac1 Crystal 11
Source: Take from hanging drop tray
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_11 | 0 | 720 | 0.1 | 7200 | 0.01 | 250 | lost higher res, detector was not very happy, stalled out at 7029 frames |
| mac1_11_bg_1 | 0 | 720 | 1 | 720 | 0.1 | 250 | went 300 µm away |
| mac1_11_bg_2 | 0 | 720 | 1 | 720 | 0.1 | 250 | went 100µm down |
Watershed, Mac1 Crystal 12
Source: Take from hanging drop tray
Relative Humidity: 90.3%
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_12 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | diffraction looks good |
| mac1_12_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 300 µm away |
| mac1_12_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100µm down |
Watershed, Mac1 Crystal 13
Source: Take from hanging drop tray
Relative Humidity: 89.3%
Notes: played with watershed - turned on temp control to see if we can get to higher humidity
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_13 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | looks good |
| mac1_13_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 250 µm away |
| mac1_13_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | 100µm down |
Watershed, Huwe1 Crystal 6
Loop size: 300 µm and still probably too small
Relative Humidity: 88.6%
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_6 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | looks good |
| huwe1_6_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | went 300 µm away |
| huwe1_6_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | went 100µm down |
Watershed, Huwe1 Crystal 7
Loop size: 300 µm and still probably too small
Relative Humidity: 88.1%
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_7 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | looks good |
| huwe1_7_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | 300 µm away |
| huwe1_7_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | went 100µm down |
Watershed, Huwe1 Crystal 8
Relative Humidity: 87.8%
Treatment: dip in Al's oil
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_8 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | diffraction is a little meh, oil background varying by frame |
Watershed, Huwe1 Crystal 9
Relative Humidity: 87.8%
Treatment: dip in Al's oil and then back in res to try to remove excess
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_9 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | crystal is all cracked, not much diffraction |
Watershed, Huwe1 Crystal 10
Relative Humidity: 87.5%
Treatment: dip in paratone oil
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_10 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | less oil background, but low res diffraction |
Watershed, Mac1 Crystal 14
Relative Humidity: 87.5%
Treatment: let paratone oil diffuse in for short time (maybe 30 s)
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_14 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | no oil background, around 360 crystal is dying and mosaicity is increasing |
| mac1_14_bg_1 | 0 | 720 | 0.1 | 720 | 0.5 | 250 | went 300µm away |
Watershed, Mac1 Crystal 15
Relative Humidity: 87.5%
Treatment: put paratone oil more on top of the drop
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_15 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | good diffraction, no background, but only shortlived, crystal is dying |
Watershed, Mac1 Crystal 16
Relative Humidity: 87.5%
Treatment: turn cryostream on and set at 297K, no oil
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_16 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | dead |
Humidity Box, Mac1 Crystal 17
Treatment: turn cryostream on and set at 297K, no oil
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_17 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | dead |
Humidity Box, Mac1 Crystal 18
Treatment: turn cryostream on and set at 297K, paratone oil diffusion, wait a little bit
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_18 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | diffraction only lasts for short time, about 150 degree |
Humidity Box, Mac1 Crystal 19
Treatment: turn cryostream on and set at 297K, dip in paratone
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_19 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | dead |
Humidity Box, Mac1 Crystal 20
Treatment: turn cryostream on and set at 297K, dip in NVH
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_20 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | no crystal ? but oil background was cleaner |
Humidity Box, Huwe1 Crystal 11
Treatment: turn cryostream on and set at 297K, dip in NVH
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_11 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | dead and cracked |
Humidity Box, Mac1 Crystal 21
Treatment: turn cryostream off, dip in NVH
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_21 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | saw some weak diffraction and then the beam went down |
Beam back
Do tune up and check transmission: 1.835 x 10¹⁰ ph/s, 1035 Gy/s
Watershed, Mac1 Crystal 22
Source: Sitting drop, put sleeve close
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_22 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | looks good, have rad damage towards the end |
| mac1_22_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 200 µm away |
| mac1_22_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100 µm down |
Humidity Box, Mac1 Crystal 23
Source: Hanging drop
Treatment: stream on 310 K
Whoops sleeve had no reservoir liquid
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_23 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | heat dehydrated the crystal |
Humidity Box, Mac1 Crystal 24
Source: Hanging drop
Treatment: stream on 310 K
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| mac1_24 | 0 | 720 | 0.1 | 7200 | 0.05 | 250 | diffraction! Some rad damage towards end as typical |
| mac1_24_bg_1 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 350 µm away |
| mac1_24_bg_2 | 0 | 720 | 1 | 720 | 0.5 | 250 | went 100 µm down |
Humidity Box, Huwe1 Crystal 12
Source: Hanging drop
Treatment: stream on 310 K
| Prefix | φ0 (deg.) | φ1 (deg.) | ∆φ (deg.) | Images | ∆t (s) | d (mm) | Notes |
|---|---|---|---|---|---|---|---|
| huwe1_12 | 0 | 360 | 0.1 | 3600 | 0.05 | 350 | diffraction!, some damage at end |
| huwe1_12_bg_1 | 0 | 360 | 1 | 360 | 0.5 | 350 | went 250 µm away, have some dried salt |
| huwe1_12_bg_2 | 0 | 360 | 1 | 360 | 0.5 | 350 | went 100 µm down, some dried salt |