Blu-Ice / DCS Toolkit: Software Components for Automated Beamlines Scott McPhillips Stanford Synchrotron Radiation Laboratory Stanford University Empty

Structural biology beam lines at SSRL BL 9-2 Crystallography BL 7-1 Crystallography (monochromatic) BL 9-1 Crystallography BL 9-3 Biological XAS BL 7-3 Biological XAS BL 11-1 Crystallography BL 11-3 Crystallography BL 1-5 Crystallography BL 4-2 Biological SAXS SPEAR3 upgrade Third-generation light source. Installation started in April Operation will resume in early ~7X lower beam emittance (18 nm-rad) ~5X smaller source size (0.4 x 0.05 mm) ~5X higher current (500 mA) Intensity increase through 0.2 mm aperture: BL 1-5: 50X (7x10 11 ph/s) BL 7-1: 15X (2x10 12 ph/s) BL 9-1: 5X (9x10 11 ph/s) BL 9-2: 20X (4x10 12 ph/s) BL11-1: 5X (4x10 12 ph/s) Macromolecular crystallography beam lines 4 multi-wavelength beam lines in operation 1 fixed wavelength beam line in operation 1 in commissioning XAS and SAXS beam lines Collect XAS data on single crystals. Collect low resolution data on SAXS line. Use Blu-Ice to collect diffraction data.

Beamline Hardware at SSRL Bl 9-2Bl 9-1Bl 11-1Bl 1-5BL 11-3 (commissioning) Area DetectorQ315 Q4 Opticsdouble crystal mono Single Crystal Horiz. Focus Single Crystal Horiz. Focus double crystal mono Single Crystal Horiz. Focus # of motors to track energy & optimize beam 3543? Sample Mounting RobotYes Auto Sample CenteringYes Motorized Fluorescence detector Yes Motorized beamsizeYes Motorized beamstop with pin diode Yes Motorized X, Y, Z detector position Yes

Dispensing Dewar 4-Axis Robot Huber Goniometer Collimator Cryo-nozzel Sample Camera Gripper Arms Hutch Table Sample Mounting Robot Commercial pick and place robot. Epson (Model ES550/320). Three vertical axis, 5 m/s Positional accuracy of 20 microns Support stand fixed to hutch table. Robot and dewar moves with energy tracking. The Dewar is easily accessible to the user.

A Compact Crystal Cassette Design details : Cassette dimensions 64mm x 130mm : Load 96 crystals per cassette on standard Hampton pins : Ship 2 cassettes inside commercial dry-shipping Dewars : Store 20 cassettes in a Taylor-Wharton HC35 storage device : Mount 3 cassettes in a dispensing Dewar at the beam line NdFeB ring magnet holds crystal securely in place Hampton magnetic base Crystal in loop

Dispensing Dewar Cassette Mounting Plate Dumbbell Magnetic Tool In Cradle Sample Cassette Dispensing Dewar Three cassette locations 288 samples available without reentering the hutch. Easy to Load Cassettes Rods poke up to just beneath the surface of the liquid nitrogen. Conical hole in the bottom of the cassette to guide the rod. Cassettes rotate easily until it locks into place on the indexing pin.

Cassette mounting plate Dumb-bell magnet tool Sample cassette Vertically opening gripper arms Fingers hold dumb-bell magnet Cryo-tong surrounds sample Dumb-bell magnet Strong magnet Weak magnet Custom robot tools Dumbell magnet tool Extracts and returns samples from the cassette while under LN2. Pneumatically operated cryo-tong Similar in function to conventional manual tongs. Surrounds the sample while in transit. Has additional set of fingers for holding dumb-bell magnet tool.

Control Software Components Authentication Server DCSS BLU-ICE(s) DHS DCS Protocol between layers TCP / IP socket based Simple text messages 3 layers decouple functionality (Blu-ICE) GUI Layer (DCSS) Distributed Control System Server Layer. Handles all tasks regarding global beamline state. Distributed Hardware Server (DHS) Layer for interfacing with hardware and other control systems. All layers have access to the authentication server. Beam Line Hardware Alternate Control System(s)

The Authentication Server Authentication Server Application Application 2 For Sofware Developers: Authentication has been decoupled from all applications. For Users: Users log in once for all applications. Applications can have buttons to spawn authenticated web pages. User can log out after system has a session Id. Application #2 Username & Password Session ID Username & SessionID Approval Username & SessionID

The Impersonation Server Authentication Server Application UserName & Password Session ID Impersonation Server The control system can start any Unix command / program as the user without adding the command to the control system software. UserName & SessionID & Unix Command UserName & SessionID Approval New process running the requested command as the User

Blu-Ice Component DCSS Beam Line Hardware BLU-ICE(s) Display layer Protocol Layer EntriesButtons Experimental Parameter Views DCS Protocol Class No global variables Configuration file for beamline specifics. DCS protocol isolated to the protocol layer. Want to try Blu-Ice with an alternate control system? Rewrite the protocol class only. DHS

Rapid GUI Development Developer Mode Embedded error reporting. Individual widgets developed separately. Application starts instantly. Standalone Blu-Ice Applications Video Only Mode Developer mode Classic Mode (full featured)

Intuitive and easy to use. Focus on experiment, not instrumentation One stop shopping for beamline control. Fully synchronized with other instances of Blu- Ice encourages collaboration. Blu-Ice Philosophy: Focus on the Experiment Incorporates 4+ years of user and support staff feedback!

DCSS Component Protect the control system and privacy of experiment Authentication via authentication server. Remote Access Restrictions Prevent remote users from moving heavy items or robot with the hutch door open. DCSS has an embedded “Scripting Engine” for handling system automation. Synchronizes multiple clients Enables collaboration among user groups and staff. No “fan-out” load on lower control system(s). DCSS BLU-ICE(s ) DHS DCSS scripts contain PX experiment knowledge and state handling. Beam Line Hardware Alternate Control System(s)

Automation with DCS: scripted devices and operations Example of scripted device hierarchy. Table Example: table_vert, table_pitch, table_pivot. slit_2_lower slit_1_vert_gap slit_2_upperslit_1_upperslit_1_lower beam_size_y slit_2_vert_gap “Real” hardware Scripted Device Legend table_vert_1 table_vert_2 table_vert table_pitch table_pivot Scripted device capabilities Scripted devices are Tcl scripts executed within DCSS. Commands are provided for starting asynchronous moves and waiting for a list of moves to complete—no need for threads! The scripts are easy for beam line staff to write, maintain, and debug. Scripted devices may be installed or modified without recompiling any part of the control system.

Scripting Engine is a Tcl interpreter executing a subset of Blu-Ice. Scripting Engine connects to DCSS Core via sockets twice. Connects to DCSS Core as a client (like Blu-Ice). Connects again as a hardware server (like a DHS). Distributed Control System Server (DCSS) Scripted devices: path of control messages Scripted device command message routing Move commands for scripted devices are routed to the Scripting Engine. Scripting Engine sends its own move commands to Core, requesting moves of real or scripted devices. DCSS Core forwards messages to external hardware servers or back to the Scripting Engine. Note that scripted devices may issue moves of other scripted devices. Blu-Ice Hardware Servers Scripting Engine Core

Scripted devices: path of response messages Scripting Engine realizes an event has occurred on a child device. Scripting Engine calculates new position of parent device and sends updates back to DCSS core. DCSS core again updates all clients All parent and children devices are updated continuously. Path of a response message DHS updates DCSS core with new motor position for real devices. DCSS core forwards updated positions to all clients including the Scripting Engine Distributed Control System Server Core Blu-Ice Hardware Servers Scripting Engine

DHS Components (Distributed Hardware Servers) Area Detectors Quantum 315 Quantum 210 (ALS port) Quantum 4 MAR CCD’s (all) MAR345 Specialized Hardware Galil 2180 DSA 2000 MCA A/D Calculations Chooch wrapper (fluorescence scans) Sample Image Analysis (JPEG sample centering) Control System Gateways ICS Control System Spear Epics (Reads Spear current PV) Epics DHS…Coming soon from GM/CA CAT DCSS BLU-ICE(s ) DHS Beam Line Hardware Alternate Control System(s) Instrument Control Area detectors Motion controllers MCA’s Etc… Abstract Task Management Perform calculations for the control system. Robot management Translation A DHS can be used to translate DCS protocols into alternate control system protocols.

Rotation angle Loop height Camera DHS for Automatic Loop Centering The “camera DHS” interface is a socket with 3 simple commands get_loop_tip – Reads image from Axis 2400 via http & returns image coordinates of extreme tip of sample. add_image_to_list – Saves current image to an indexed list in memory. find_bounding_box- Analyzes list of images and finds a 3- D bounding box for the loop. The “camera DHS” only tells you what it sees. It does not move motors.

DCSS Blu-Ice Motor moves Image operations Center loop Sample loop centering (Simplified system view) Operations may be implemented as Tcl scripts in DCSS: scripted operations. The center_loop scripted operation contains the logic for centering a sample loop automatically. Starts and waits for operations provided by the camera DHS. Moves goniometer and sample motors as needed to center loop. center_loop Axis 2400 Galil 2180 Sample camera Camera DHSMotor DHS The centering algorithm is documented in one place…The scripting engine.

Robot DHS The interface is a socket with simple commands. “mount” “dismount” “mount next” “move” (Moves from one port to another) “standby”, “configure”, & “calibrate” Robot can self calibrate using the force sensor. Magnet transfer post Goniometer head 3 Cassette locations The “Robot DHS” can be used as a standalone program. Z U θ1θ1 θ2θ2 Epson ES553 Robot Built in sanity checks & performance monitoring Restricts movement of sample to occupied port. Verifies sample returned to port successfully ( force sensor). Detects poor calibration (force sensor).

Blu-Ice interface for crystal screening Import user crystal data Organize data: generate paths and file names automatically Automate execution of experiment Specify minimal parameters

Automated Sample Screening (Simplified System View) Screening Operation: Moves detector_z, beamstop, gonio_phi, sample_x, sample_y, and sample_z Calls Robot “mount” and “dismount” for sample. Calls the center loop script. Calls diffraction image script. Snaps a JPEG image of sample and stores it in the Users directory (via Impersonation DHS). Screening Operation Imp DHSMotor DHS Center LoopCollect Diffraction DCSS Detector DHSRobot DHS Mount Sample The screening algorithm is documented in one place…The scripting engine.

Example Screening Results

Automated MAD Experiment (Simplified System View) DCSS Motor moves & Flourescence Readings Scan Data Mad Scan User: User selects heavy atom from periodic table. Mad Scan Operation: Positions fluorescence detector for optimal % dead time. Scans energy with fluorescence detector. Calls impersonation DHS with the raw scan data. Impersonation DHS: Runs chooch as the user and places files in their directory. Returns inflection, peak, and remote. Returns names of files of smoothed data, fp fpp graphs. All instances of Blu-Ice can load the results for display. Mad Scan Operation Auto Chooch Process Fluorescence_z, Energy Impersonation DHSMotor DHS

Automating MAD Experiments Automatically optimize signal and perform fluorescence scan Automatically analyze the absorption edge with a modified version of Chooch Select heavy atom from a periodic table Automatically select energies for MAD experiment and complete data collection definition

Open protocol. Open architecture. Open source. Free! MIT-style free software license. No restrictions on use. Free All code stored in CVS (Concurrent Version System) Access current or past versions. Request a password to the SSRL CVS repository from External collaborators can see developments at SSRL. Online Documentation DCS Administrator’s Manual Script Writer’s Guide

The Macromolecular Crystallography Group SSRL is funded by: Department of Energy, Office of Basic Energy Sciences The Structural Molecular Biology Program is supported by: National Institutes of Health, National Center for Research Resources,Biomedical Technology Program NIH, National Institute of General Medical Sciences and by the Department of Energy, Office of Biological and Environmental Research. SSRL Director Keith Hodgson SMB Leader Britt Hedman MC Leader Mike Soltis