Toward the automation ofbiological structure determination

Thomas EarnestBerkeley Center for Structural Biology

Physical Biosciences DivisionLawrence Berkeley National Laboratory

Manual mounting and alignment

sample

dewar

goniometer/

XYZ stage

micro-scope

cryostream

gripper

heater

collimator/

beamstop

Crystal transport and handling

automounterdewar with 112

samples

sample cassette with magnetic base (puck)

puck handling tools

Crystal transport and storage

Taylor-WhartonCP 100 dry shipping

Dewar holds 7 pucks (112 samples)

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

This system is installed and operational onBL 5.0.1, 5.0.2, 5.0.3

Under construction for HHMI BL 8.2.1

Also under construction for beamlines atNSLS, CHESS, and APS SER-CAT

97.197.096.9

2018161412108642

Dataset

188.8188.7188.6

45.745.645.5

57.0

56.5

56.0

42.041.0

5.0

4.5

60.050.040.0

11.010.0

9.0

1.61.41.21.0

-55.0

-50.0

-45.0

1.1

1.0

0.9

a

b

c

last shell

all

all

all

last shell

last shell

Beamline software DCS: Hutch Tab

Beamline Software DCS: Scan Tab

Beamline software DCS: Track Tab

Autonomous agents as real-time,adaptive controllers of

•Data collection•Data processing•Analysis•Process flow•Information analysis

ROBOHUTCH CYBERHUTCH

Automated screening / data collection

• Crystal mounting

• Centering

• Screening

• Rescreen

• Unmounting

Collaboration between BCSB and CCI (P. Adams, Nick Sauter)

Data collection on best crystal:

Mounting/Collecting/Unmounting

userpriority score

strategy

Sample Comments Bravais Lattice Mosaicity Distance x-Beam y-Beam rms Residual Resolutionalpha-lytic protease P3 0.15 130.4 172.7 172.3 0.034 0.89

lysozyme P4 0.54 198.7 94.1 99.3 0.043 1.98lysozyme P4 0.78 198.7 94.1 99.2 0.105 1.88lysozyme P4 0.40 198.9 94.1 99.5 0.070 1.88

mercury derivative C222 0.50 198.4 90.7 94.0 0.059 2.14y114: large unit cell P4 0.70 220.1 99.5 95.7 0.096 2.29

poorly diffracting lysozyme peculiar back ground; possible ice ring/iteration limitpoorly diffracting lysozyme two segments autoindex to different Laue groups/iteration limitpoorly diffracting lysozyme peculiar back ground; possible ice ring/iteration limit

crystal looks twinned two segments autoindex to different Laue groups/iteration limitblank image peculiar back ground; possible ice ring/iteration limitblank image invalid back ground with average counts too low/iteration limit

Xtal / User db

environmentagent

?

sensors

actuators

Autonomous agents

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

•situated within and a part of an environmentbeamline, automounter, computational control

•senses that environmentoptical system, encoders

•acts on itmount crystalmove goniometer, detector

take data

•pursuit of its own agendacollection of highest-quality data as fast as possiblestructure determination

•effect what it senses in the futureknowledge base updating and influencing future actions

Carl Cork Bob NordmeyerJohn Taylor Earl CornellGyorgy Snell BioinstrumentationJeff DickertBrian Greensmith Azer Dauz Nick SauterToni Borders Paul AdamsAnthony Rozales CCIJon SpearsBCSB

NIH/NIGMS, DOE/OBER, Agouron Institute