1. Toward the automation of biological structure determination
Thomas Earnest
Berkeley Center for Structural Biology
Physical Biosciences Division
Lawrence Berkeley National Laboratory

2. Manual mounting and alignment

3. micro-scope
cryostream
gripper
goniometer/
XYZ stage
collimator/
beamstop
dewar
heater
sample

5. Crystal transport and handling
sample cassette with magnetic base (puck)
puck handling
tools
automounter dewar with 112 samples

6. Crystal transport and storage
Taylor-Wharton
CP 100 dry shipping
Dewar holds 7 pucks
(112 samples)

7. Automated Loop Alignment
Auto Focus if loop can’t be found (<10 sec)
Center Loop (2 sec)
Rotate 90 degrees (1 sec)
Center Loop (2 Sec)
Raster using low-dose x-rays to maximize diffraction, thus centering xtal

10. This system is installed and operational on
BL 5.0.1, 5.0.2, 5.0.3
Under construction for HHMI BL 8.2.1
Also under construction for beamlines at
NSLS, CHESS, and APS SER-CAT

12. Beamline software DCS: Hutch Tab

14. Beamline Software DCS: Scan Tab

15. Beamline software DCS: Track Tab

16. Autonomous agents as real-time,
adaptive controllers of
Data collection
Data processing
Analysis
Process flow
Information analysis
ROBOHUTCH CYBERHUTCH

17. Automated screening / data collection
Collaboration between BCSB and CCI (P. Adams, Nick Sauter)
• Crystal mounting
• Centering
• Screening
• Rescreen
• Unmounting
Data collection on best crystal:
Mounting/Collecting/Unmounting
user
priority
score
strategy

18. Xtal / User db

19. Autonomous agents
environment
agent ?
sensors
actuators

20. Autonomous Agents Definition:
“An autonomous agent is a system situated within and a part of an environment that senses that environment and acts on it, over time, in pursuit of its own agenda and so as to effect what it senses in the future.”
Franklin & Graesser, 1996
“Is it an Agent, or just a Program?”
Proc. of 3rd Int. Workshop on Agent Theories

21. situated within and a part of an environment
beamline, automounter, computational control
senses that environment
optical system, encoders
acts on it
mount crystal
move goniometer, detector
take data
pursuit of its own agenda
collection of highest-quality data as fast as possible
structure determination
effect what it senses in the future
knowledge base updating and influencing future actions

22. NIH/NIGMS, DOE/OBER, Agouron Institute
Carl Cork Bob Nordmeyer
John Taylor Earl Cornell
Gyorgy Snell Bioinstrumentation
Jeff Dickert
Brian Greensmith
Azer Dauz Nick Sauter
Toni Borders Paul Adams
Anthony Rozales CCI
Jon Spears
BCSB
NIH/NIGMS, DOE/OBER, Agouron Institute