Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Beam Time Allocation Plexxikon UC Berkeley 25% 5% 10% 8%

Beam Time Allocation UC Berkeley 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 PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Funding for ALS FY 2006 costTotal costEnd date ContractsU Alberta$200,000$800,00001/07 MD Anderson$116,000$748,00007/08 Plexxikon$150,000$1.25 M02/07 UCSD$35,000$145, GrantsUCSF NIH Center grant $80,000$320,0006/10 DOE IDAT (SIBYLS)$84,000TBD9/09 NIH STTR (Fluidigm)$28,200$141,0007/08 Total$693,200$3.4 M-

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

ADSC Quantum 210 X-ray optics Superbend Plane Parabolic mirror Torroidal mirror Si(111) monochromator Protein Crystal pinhole Scatter guard 2:1 demagnification cancels spherical aberrations comparable flux to a wiggler with < 1% of the heat divergence slits

ADSC Quantum 210 X-ray optics Superbend Plane Parabolic mirror Torroidal mirror Si(111) monochromator Protein Crystal pinhole Scatter guard 2:1 demagnification cancels spherical aberrations comparable flux to a wiggler with < 1% of the heat divergence slits

Zero-parallax optics pinhole prism microscope Styrofoam™ backlight backstop

Zero-parallax optics pinhole prism microscope Styrofoam™ backlight backstop

Background scattering at Resolution (Ǻ) Photons/s/pixel Se edge with detector at 100 mm 

Future plan: reduce background Laser machining of cold protein crystal H. Kitano et. al. Jpn. J. Appl. Phys. 44,2 L 54–L 56 (2005)

Future plan: optimize samples Laser machining of cold protein crystal H. Kitano et. al. Jpn. J. Appl. Phys. 44,2 L 54–L 56 (2005)

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline 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 Envelope Radiation Safety System (RSS) Personnel Protection System (PSS) Equipment Protection System (EPS) GERT Training Training experiment

Safety Envelope Radiation Safety System (RSS) Personnel Protection System (PSS) Equipment Protection System (EPS) GERT Training 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

Detector retraction ADSC Quantum 210

Detector retraction ADSC Quantum 210

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 2003 MOTOROLA 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 Distraction is unsafe! Distance from the lead vehicle (secs.) Median time to lift foot off accelerator (secs.) Distraction Condition No-Distraction Condition Distance from the lead vehicle (secs.) Median time to lift foot off accelerator (secs.) Distraction Condition No-Distraction Condition 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 PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline 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

DCS server SSRL DCS 3.0 at the ALS beamline Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

Touch screen

DCS server SSRL DCS 3.0 at the ALS beamline Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

DCS server SSRL DCS 3.0 at the ALS beamline Energy Divergence steering Foils plungers lights Detector Collimator beamstop Spindle Goniometer shutter ADSC Q210 detector DHS Wago DHS PMAC1 DHS PMAC2 DHS LabView DHS

Integration of Elves with BLU-ICE Elves structure solution data collection index Wedger Elves mosflm autoindex strategy most recent image run information

Integration of Elves with BLU-ICE Elves structure solution data collection process run information pick un-busy cluster node mosflm scala solve ARP/wARP

ALS beamline health monitor

ALS lN 2 health monitor

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

Beamline PRT organization Funding Hardware Safety management Control system Scientific productivity

How many are we solving? Jiang & R.M. Sweet (2004)

SecondsDescriptionPercent Assigned and available91% 42093Shutter open40% 52684Collecting (3026 images)50% 51806Something else50% Operational Efficiency “representative” user

SecondsDescriptionPercent 51806Something else100% 247s  45 Mounting22% 229s  37 Centering16% 179s  109 Strategizing38% 309s  37 Prepping24% Operational Efficiency “representative” user

NumberDescriptionPercent Images (~7 TB)33% 2346Data sets47% 449MAD/SAD (1:2)19% 48Published2% in 2003 Turning data into models

Top producing beamlines of the world Structures credited

Top producing beamlines of the world x10 6 unique HKLs

Top producing beamlines of the world Structures/10 20 photons

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 Elven Automation 148datasets 117succeded ~3.5 (0.1-75)hours 31 failed ~61 (0-231)hours 2 / 15MAD 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 Elven Automation 148datasets 117succeded ~3.5 (0.1-75)hours 31failed ~61 (0-231)hours 2 / 15MAD structures

“What is a good exposure time?”

“How much signal do I need?”

Is it real, or is it MLFSOM ?

MAD phasing simulation Anomalous signal to noise ratio Correlation coefficient to correct model mlphare results

SAD phasing simulation Anomalous signal to noise ratio Correlation coefficient to correct model mlphare results

Minimum required signal (MAD/SAD)

SAD phasing experiment Anomalous signal to noise ratio Correlation coefficient to published model

“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 Absorbed dose (MGy) Water ring position (Ǻ) saturated sucrose in 250mM WO4

Water ring shift bubbles? Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)

Water ring shift Hydrogen bubbles? Richard D. Leapman, Songquan Sun, Ultramicroscopy (1995)

Specific Damage

Individual atoms decay at different rates dose (MGy) Correlation coefficient to observed data

Damage changes absorption spectrum Photon energy (eV) counts 1 0

fluorescence probe for damage fluence (10 15 photons/mm 2 ) Fraction unconverted 25mM SeMet in 25% glycerol Exposing at eV

fluorescence probe for damage fluence (10 15 photons/mm 2 ) Fraction unconverted 25mM SeMet in 25% glycerol Exposing at eV Se cross-section at eV

fluorescence probe for damage Absorbed Dose (MGy) Fraction unconverted Wide range of decay rates seen Half-dose = 41.7 ± 4 MGy “GCN4” in crystal Half-dose = 5.5 ± 0.6 MGy 8 mM SeMet in NaOH Protection factor: 660% ± 94%

Scientific highlights