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Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beam Time Allocation
UC Berkeley25%
25%
25%10%
8%
5%
2%
Plexxikon
General User Program
Staff
George Meigs
Senior Research Associate
James Holton
Beamline Director
Jane Tanamachi
Administrator
Tom Alber
Principal Investigator
PRT
Member Labs
PRT
Contractees
Staff
Group photo?
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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 -
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
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
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
Zero-parallax optics
pinhole
prism
microscope
Styrofoam™ backlight
backstop
Zero-parallax optics
pinhole
prism
microscope
Styrofoam™ backlight
backstop
Background scattering at 8.3.1
0
50
100
150
200
250
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
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Safety Management
• Hardware safety systems• Training• Safety through simplicity• Failsafe envelope
• Examples:– Liquid nitrogen – better tools– Automatic retraction – eliminate confusion– Automatic backup – eliminate distraction
Safety EnvelopeRadiation Safety System (RSS)
Personnel Protection System (PSS)
Equipment Protection System (EPS)
GERT Training 8.3.1 Training
experiment
Safety EnvelopeRadiation Safety System (RSS)
Personnel Protection System (PSS)
Equipment Protection System (EPS)
GERT Training 8.3.1 Training
experiment
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
Example 1: Liquid nitrogen
Liquid nitrogen safety concern
A safer way
Safer and more productive!
Example 2: Automatic detector retraction
ADSC Quantum 210
ADSC Quantum 210
Detector retraction
ADSC Quantum 210
Detector retraction
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
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.
Automated firewire drive backup
Automated DVD archive
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
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Software
BLU-ICE 3.0 control system
Elves integrated with BLU-ICE
ALS-wide beamline health monitor
DCS server
SSRL DCS 3.0
DHS DHS
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
Touch screen
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
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
Integration of Elves with BLU-ICE
Elvesstructure solution
data collection
index
Wedger Elves
mosflmautoindexstrategy
most recent im
age
run information
Integration of Elves with BLU-ICE
Elvesstructure solution
data collection
process
run information
pickun-busyclusternode
mosflmscalasolve
ARP/wARP
ALS beamline health monitor
ALS lN2 health monitor
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
Beamline 8.3.1
PRT organization
Funding
Hardware
Safety management
Control system
Scientific productivity
How many are we solving?
Jiang & R.M. Sweet (2004)
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
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
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
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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
avoiding overlaps
c
c
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
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
Is it Is it realreal, or is it , or is it MLFSOMMLFSOM??
MAD phasing simulation
-0.2
0
0.2
0.4
0.6
0.8
1
0.01 0.1 1 10
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t m
odel
mlphare results
SAD phasing simulation
-0.2
0
0.2
0.4
0.6
0.8
1
0.01 0.1 1 10
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o co
rrec
t m
odel
mlphare results
Minimum required signal (MAD/SAD)
"#
)(3.1
fsitesDaMW
sd
I
SAD phasing experiment
0.0
0.1
0.2
0.3
0.4
0.5
0.6
0.5 1.0 1.5 2.0 2.5 3.0
Anomalous signal to noise ratio
Cor
rela
tion
coef
ficie
nt t
o pu
blis
hed
mod
el
“We really need those
high-resolution spots”
Incremental strategy
incremental_strategy.com merged.mtz auto.mat
“We have a problem with
non-isomorphism”
Proteins move
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
Overlaps
Signal to noise
Radiation Damage
Why do structures fail?
thaw
Radiation Damage
Lattice damage
Distention of cryo with dose
before
beam
Distention of cryo with dose
after
beam
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
Water ring shiftbubbles?
Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)
Water ring shiftHydrogen bubbles?
Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)
Specific Damage
Specific Damage
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
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
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
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
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%
Scientific highlights
