beamline 8.3.1 prt organization funding hardware safety management control system scientific...

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