Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific...
Transcript of Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific...
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 3: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/3.jpg)
Beam Time Allocation
UC Berkeley25%
25%
25%10%
8%
5%
2%
Plexxikon
General User Program
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Staff
George Meigs
Senior Research Associate
James Holton
Beamline Director
Jane Tanamachi
Administrator
Tom Alber
Principal Investigator
PRT
Member Labs
PRT
Contractees
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Staff
Group photo?
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 7: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/7.jpg)
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 8: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/8.jpg)
Funding for ALS 8.3.1
FY 2006 cost Total cost End date
Contracts U Alberta $200,000 $800,000 01/07
MD Anderson $116,000 $748,000 07/08
Plexxikon $150,000 $1.25 M 02/07
UCSD $35,000 $145,000 2011
Grants UCSF NIH Center grant
$80,000 $320,000 6/10
DOE IDAT (SIBYLS) $84,000 TBD 9/09
NIH STTR (Fluidigm) $28,200 $141,000 7/08
Total $693,200 $3.4 M -
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 10: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/10.jpg)
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 11: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/11.jpg)
AD
SC
Qu
antu
m 2
10
X-ray opticsSuperbend
PlaneParabolic
mirror
Torroidalmirror
Si(111)monochromator
Protein Crystal
pinhole Scatterguard
• 2:1 demagnification cancels spherical aberrations
• comparable flux to a wiggler with < 1% of the heat
divergenceslits
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AD
SC
Qu
antu
m 2
10
X-ray opticsSuperbend
PlaneParabolic
mirror
Torroidalmirror
Si(111)monochromator
Protein Crystal
pinhole Scatterguard
• 2:1 demagnification cancels spherical aberrations
• comparable flux to a wiggler with < 1% of the heat
divergenceslits
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Zero-parallax optics
pinhole
prism
microscope
Styrofoam™ backlight
backstop
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Zero-parallax optics
pinhole
prism
microscope
Styrofoam™ backlight
backstop
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Background scattering at 8.3.1
0
50
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150
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300
0.00 0.07 0.13 0.20 0.27 0.33 0.40 0.47
35mm air
200um water
everything else
Resolution (Ǻ)
Ph
oto
ns/
s/p
ixel
Se edge with detector at 100 mm
7.5 3.8 2.5 1.9 1.5 1.2 1.1
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
![Page 17: Beamline 8.3.1 PRT organization Funding Hardware Safety management Control system Scientific productivity.](https://reader036.fdocuments.us/reader036/viewer/2022062314/56649ea75503460f94ba9a78/html5/thumbnails/17.jpg)
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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Safety Management
• Hardware safety systems• Training• Safety through simplicity• Failsafe envelope
• Examples:– Liquid nitrogen – better tools– Automatic retraction – eliminate confusion– Automatic backup – eliminate distraction
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Safety EnvelopeRadiation Safety System (RSS)
Personnel Protection System (PSS)
Equipment Protection System (EPS)
GERT Training 8.3.1 Training
experiment
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Safety EnvelopeRadiation Safety System (RSS)
Personnel Protection System (PSS)
Equipment Protection System (EPS)
GERT Training 8.3.1 Training
experiment
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Safety Envelope
“There is no safety system that can stop a determined user with a hacksaw”
-Anonymous
Solution:
Create tools that enhance productivity within the safety envelope
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Example 1: Liquid nitrogen
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Liquid nitrogen safety concern
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A safer way
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Safer and more productive!
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Example 2: Automatic detector retraction
ADSC Quantum 210
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ADSC Quantum 210
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Detector retraction
ADSC Quantum 210
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Detector retraction
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Automatic detector retraction
• Detector motors are disabled with hutch door open (pinch hazard)
• Sample is difficult to access with detector in data collection position
• Common mistake: – forget to retract detector before opening door
• Result: confusion• Solution:
– Door will not open with detector forward– Detector automatically retracts on door open attempt
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March 2003MOTOROLA and the Stylized M Logo are registered in the US
Patent & Trademark Office. All other product or service names are the property of their respective owners.
© Motorola, Inc. 2002.
Distraction is unsafe!Distraction is unsafe!
0.8
1.0
1.2
1.4
1.6
1.8
2 4 6 8
Distance from the lead vehicle (secs.)
Me
dia
n t
ime
to
lif
t fo
ot
off
ac
ce
lera
tor
(se
cs
.)
DistractionCondition
No-DistractionCondition
0.8
1.0
1.2
1.4
1.6
1.8
2 4 6 8
Distance from the lead vehicle (secs.)
Me
dia
n t
ime
to
lif
t fo
ot
off
ac
ce
lera
tor
(se
cs
.)
DistractionCondition
No-DistractionCondition
Drivers following a car that suddenly brakes take longer to respond to that event when they are distracted by trying to solve a logic problem. This is especially true if the two vehicles start out close together--when it is critical that the driver in the following vehicle make a rapid response to avoid a rear-end collision.
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Automated firewire drive backup
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Automated DVD archive
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Safety Summary
• Encourage safe practices by making them the best way to get results
• Measures are in addition to existing ALS safety envelope
• Better science and better safety go hand in hand
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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Software
BLU-ICE 3.0 control system
Elves integrated with BLU-ICE
ALS-wide beamline health monitor
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DCS server
SSRL DCS 3.0
DHS DHS
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DCS server
SSRL DCS 3.0 at the ALS beamline 8.3.1
EnergyDivergence
steering
Foilsplungers
lights
DetectorCollimatorbeamstop
SpindleGoniometer
shutter
ADSC Q210
detectorDHS
WagoDHS
PMAC1DHS
PMAC2DHS
LabViewDHS
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Touch screen
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DCS server
SSRL DCS 3.0 at the ALS beamline 8.3.1
EnergyDivergence
steering
Foilsplungers
lights
DetectorCollimatorbeamstop
SpindleGoniometer
shutter
ADSC Q210
detectorDHS
WagoDHS
PMAC1DHS
PMAC2DHS
LabViewDHS
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DCS server
SSRL DCS 3.0 at the ALS beamline 8.3.1
EnergyDivergence
steering
Foilsplungers
lights
DetectorCollimatorbeamstop
SpindleGoniometer
shutter
ADSC Q210
detectorDHS
WagoDHS
PMAC1DHS
PMAC2DHS
LabViewDHS
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Integration of Elves with BLU-ICE
Elvesstructure solution
data collection
index
Wedger Elves
mosflmautoindexstrategy
most recent im
age
run information
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Integration of Elves with BLU-ICE
Elvesstructure solution
data collection
process
run information
pickun-busyclusternode
mosflmscalasolve
ARP/wARP
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ALS beamline health monitor
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ALS lN2 health monitor
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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How many are we solving?
Jiang & R.M. Sweet (2004)
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Seconds Description Percent
104490 Assigned and available 91%
42093 Shutter open 40%
52684 Collecting (3026 images) 50%
51806 Something else 50%
Operational Efficiency“representative” 8.3.1 user
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Seconds Description Percent
51806 Something else 100%
247s 45 Mounting 22%
229s 37 Centering 16%
179s 109
Strategizing 38%
309s 37 Prepping 24%
Operational Efficiency“representative” 8.3.1 user
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Number Description Percent
446028 Images (~7 TB) 33%
2346 Data sets 47%
449 MAD/SAD (1:2) 19%
48 Published 2%
8.3.1 in 2003
Turning data into models
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
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avoiding overlaps
c
c
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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Apr 6 – 24 at ALS 8.3.1
Elven Automation
148 datasets
117 succeded
~3.5 (0.1-75) hours
31 failed
~61 (0-231) hours
2 / 15 MAD structures
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Is it Is it realreal, or is it , or is it MLFSOMMLFSOM??
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MAD phasing simulation
-0.2
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Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t m
odel
mlphare results
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SAD phasing simulation
-0.2
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Anomalous signal to noise ratio
Cor
rela
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coef
ficie
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o co
rrec
t m
odel
mlphare results
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Minimum required signal (MAD/SAD)
"#
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sd
I
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SAD phasing experiment
0.0
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Anomalous signal to noise ratio
Cor
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tion
coef
ficie
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o pu
blis
hed
mod
el
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“We really need those
high-resolution spots”
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Incremental strategy
incremental_strategy.com merged.mtz auto.mat
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“We have a problem with
non-isomorphism”
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Proteins move
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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thaw
Radiation Damage
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Lattice damage
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Distention of cryo with dose
before
beam
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Distention of cryo with dose
after
beam
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Water ring shift
3.555
3.565
3.575
3.585
3.595
3.605
3.615
0 10 20 30 40 50 60
Absorbed dose (MGy)
Wat
er r
ing
posi
tion
(Ǻ)
saturated sucrose in 250mM WO4
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Water ring shiftbubbles?
Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)
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Water ring shiftHydrogen bubbles?
Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)
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Specific Damage
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Specific Damage
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Individual atoms decay at different rates
00.10.20.30.40.50.60.70.80.9
1
0 20 40 60 80 100
all atoms
Se #1
Se #5
dose (MGy)
Cor
rela
tion
coef
ficie
nt t
o ob
serv
ed d
ata
0 12 24 36 48 60
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Damage changes absorption spectrum
0
500
1000
1500
2000
2500
3000
3500
4000
4500
50001
26
40
12
64
5
12
65
0
12
65
5
12
66
0
12
66
5
12
67
0
12
67
5
12
68
0
12
68
5
12
69
0
12
69
5
12
70
0
beforebeforeburntburnt
Photon energy (eV)
coun
ts
1
0
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fluorescence probe for damage
fluence (1015 photons/mm2)
Fra
ctio
n u
nco
nve
rted
25mM SeMet in 25% glycerol
0.
0
0
.2
0.4
0.6
0
.8
1.0
0 50 100 150 200 250 300 350 400
Exposing at 12680 eV
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fluorescence probe for damage
fluence (1015 photons/mm2)
Fra
ctio
n u
nco
nve
rted
25mM SeMet in 25% glycerol
0.
0
0
.2
0.4
0.6
0
.8
1.0
0 50 100 150 200 250 300 350 400
Exposing at 12680 eV
Se cross-section at 12680 eV
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fluorescence probe for damage
Absorbed Dose (MGy)
Fra
ctio
n u
nco
nve
rted
Wide range of decay rates seen
0.
0
0
.2
0.4
0.6
0
.8
1.0
0 50 100 150 200
Half-dose = 41.7 ± 4 MGy“GCN4” in crystal
Half-dose = 5.5 ± 0.6 MGy8 mM SeMet in NaOH
Protection factor: 660% ± 94%
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Scientific highlights