Rigaku Phoenix HT User manual

Phoenix HT
User Manual
May 2012
401718 Rev A
TM

Phoenix HT User Manual
© 2007–2012 Rigaku Automation, Inc. ii 401718 Rev A
Copyright
Copyright © 2007-2012 Rigaku Corporation and/or Rigaku Americas Corporation (Rigaku). All rights
reserved.
No part of this publication may be stored in a retrieval system, transmitted or reproduced in any way,
including but not limited to photocopy, photography, magnetic or other record without prior written permission
of Rigaku. To order additional copies of this publication, request this manual part number (shown at the top of
this page) from your authorized Rigaku service center.
This publication may contain or reference information concerning or related to products protected by either
copyrights or patents (or both) and does not convey any license under the patent rights of Rigaku nor the
rights of others. Rigaku does not assume any liabilities arising out of any infringements of patents or other
rights of third parties.
Disclaimer
Rigaku reserves the right to change its products and services at any time to incorporate technological
developments. This manual is subject to change without prior notice as part of a continuous product
development. Although this manual has been prepared with every precaution to ensure accuracy, Rigaku
assumes no liability for any errors or omissions, nor for any damages resulting from the application or use of
this information. Except as specifically set forth in its terms and conditions of sale, Rigaku makes no warranty
of any kind with regard to this document, including, but not limited to, the implied warranties of merchantability
and fitness for a particular purpose. Rigaku shall not be liable for errors contained herein for incidental
consequential damages in connection with furnishing, performance or use of this material. This manual
supersedes all previous editions.
Rigaku shall not be liable for any damages whatsoever arising out of the use or misuse of the product(s)
covered by this document.
Trademarks
Phoenix DT, Phoenix HT, Minstrel, Gallery, CrystalTrak, and CrystalMation are trademarks of Rigaku
Automation, Inc. All other trademarks and registered trademarks are sole property of their respective owners.
Document
Part Description: Phoenix HT User Manual
Part Number: 401718
Revision Letter: A
Publication Date: 05-30-2012
Any comments about the documentation for this product should be emailed to: [email protected] or
addressed to:
Rigaku Americas Corporation
Attn: MARCOM Group
9009 New Trails Drive
The Woodlands, TX 77381 U.S.A.
Software
ARI Phoenix Version: 1.10.3.2
CrystalTrak Version 2.3.37 (DB v3.0.2)
Authorized EU Representative:
Rigaku Europe
Unit B6 Chaucer Business Park, Watery Lane,, Kemsing, SEVENOAKS, Kent TN15 6QY
011 44 1732 763367

© 2007–2012 Rigaku Automation, Inc. iii 401718 Rev A
Table of Contents
Preface ........................................................................................................................v
CHAPTER 1. INTRODUCTION ........................................................................................1
1.1. General Description ...................................................................................... 1
1.2. Phoenix HT System Major Components ......................................................... 2
1.2.1 Phoenix Base System .............................................................................. 2
1.2.2 Enclosure Status Light Indicators ............................................................ 3
1.2.3 Protein Chiller Block ............................................................................... 3
1.2.4 Wash Stations ......................................................................................... 5
1.2.5 Nano-Dispense Controller ...................................................................... 6
1.2.6 Anti-Static Bar ........................................................................................ 7
1.2.7 Active Nest ............................................................................................. 7
1.2.8 Plate and Shelf Sensors ........................................................................... 8
1.2.9 Active Nest Terminals ............................................................................. 8
1.3. Safety Features ............................................................................................. 8
1.4. Potential Hazards .......................................................................................... 9
1.4.1 Networking ............................................................................................ 9
1.4.2 Electric Power Hazards ........................................................................... 9
1.4.3 Moving the Phoenix HT System from Cold to Warm Areas ....................... 9
1.5. Rigaku Service and Support .......................................................................... 9
CHAPTER 2. BASICS ..................................................................................................11
2.1. System Power-On ....................................................................................... 11
2.2. Shutting Down the System ......................................................................... 12
2.3. Running the System .................................................................................... 12
2.4. Status Light Indicators ................................................................................ 12
2.5. Using the Stop, Start, and Emergency Stop (EMO) Pushbuttons .................... 13
2.6. Resetting the System after an Emergency Motor Off (EMO) Shutdown .......... 13
CHAPTER 3. QUICK START PROCEDURES ....................................................................14
3.1. Preliminary Setup ....................................................................................... 14
3.2. Phoenix HT Software Procedures ................................................................. 15
CHAPTER 4. PHOENIX HT APPLICATION REFERENCE ....................................................19
4.1. Organization ............................................................................................... 19
4.2. File Menu .................................................................................................... 20
4.3. View Menu .................................................................................................. 20
4.4. Jobs Menu ................................................................................................... 20
4.5. Tools Menu ................................................................................................. 21
4.6. Help Menu .................................................................................................. 23
4.7. Views Pane and Icons .................................................................................. 23
4.8. Jobs View .................................................................................................... 23
4.9. Manage Device View ................................................................................... 24
4.9.1 Chilled Block and Ambient Block Tabs .................................................. 24
4.9.2 Onboard Plates Tab .............................................................................. 25
4.10. Job History View ......................................................................................... 26

Phoenix HT User Manual
© 2007–2012 Rigaku Automation, Inc. iv 401718 Rev A
CHAPTER 5. MAINTENANCE .......................................................................................28
5.1. Scheduled Maintenance .............................................................................. 28
5.2. Equipment Cleaning .................................................................................... 28
5.3. Daily Detergent Wash Required ................................................................... 28
5.4. Replacing the Nano-Tip Valve Harness Assembly ........................................ 30
5.4.1 Removing the Nano-Tip Valve Harness ................................................. 30
5.4.2 Installing the Replacement Nano Valve Harness .................................... 33
5.5. Calibrating the Nano Dispenser .................................................................. 35
5.6. Aligning the Nano Dispenser ....................................................................... 37
Options and Spare Parts ............................................................................................39
Facilities Layout and Cabling .....................................................................................40
Revision History ........................................................................................................48
Index ........................................................................................................................49

© 2007–2011 Rigaku Automation, Inc. v401718 Rev A
Preface
The Preface provides documentation conventions, icons, and terminology used throughout this
manual.
Warning and Caution Notices
This manual uses the icons and typographic conventions described and illustrated here.
WARNING
Warnings alert you to situations that could result in serious personal injury or loss of
life.
AVERTISSEMENT
Les avertissements vous alertent aux situations qui pourraient avoir comme
conséquence des blessures ou perte ou vie sérieuse.
WARNING
WARNING alarmieren Sie zu den Situationen, die ernste Personenschäden oder Verlust
oder Lebensdauer ergeben konnten.
ALERTA
Las alertas le alertan a las situaciones que podrían dar lugar a daños corporales o a
pérdida o a vida seria.
CAUTION
Cautions indicate situations that can damage the machine.
ATTENTION
Les attentions indiquent les situations qui peUV ent endommager la machine.
VORSICHT
Vorsicht zeigen Situationen an, die Maschine beschädigen können.
PRECAUCIÓN
Las precauciones indican las situaciones que pueden dañar la máquina.
Risk of Electric Shock
Risque électrique de décharge
Gefahr des elektrischen Schlages
Riesgo eléctrica de la descarga
Protected Earth Ground

© 2007–2011 Rigaku Automation, Inc. vi 401718 Rev A
Part Names
Parts of the software appear in the manual with the first letter of the word capitalized and the
entire word in italics. Thus, “job” refers to something the operator or system would do, but “Job”
refer to a software component.
Terminology
This section presents descriptions and definitions of terms used in this document.
A chemical is a substance that can be purchased. A chemical probably has a CAS number
associated with it. The units of measurement suggest the phase or type of the chemical and the
information required, for example:
Units of M suggest an ionic solid (for example, ammonium sulfate)
Information required: formula weight, default stock, solubility, ionic makeup
Units of %w/v suggest a polymer (for example, PEG 3350)
Information required: default stock
Units of %v/v suggest a liquid (for example, Dioxane)
Information required: density
A Sample is a specific preparation of the protein that is set up in a crystallization experiment.
For example, a Sample could be 25mg/ml lysozyme in acetate, 50% BSA.
Astock is a liquid that is used in the lab:
NaCl is a chemical
5M NaCl is a stock
A default stock is generally the concentration of the aqueous solution of a chemical that is sold
by Hampton Research.
A reservoir design is a collection of chemicals that make up the reservoirs of a plate.
A standard screen is a crystallization screen that can be purchased from outside vendors.
A drop design is a collection of chemicals in the crystallization drop. A drop may consist of a
protein sample and a reservoir, or a protein sample and any collection of chemicals.
A sitting drop experiment is a vapor diffusion experiment with a reservoir design associated
with it.
A hanging drop experiment is a vapor diffusion experiment with a reservoir design associated
with it.
An oil experiment is a microbatch experiment with a sets of drop parameters and a volume of
oil associated with it.
A recipe is the set of instructions for preparing the chemicals specified by a design for
reservoirs and drops of a plate, including the quantities of stocks used in each.
A class is a classification for the chemicals used in the CrystalTrak database. Salt, polymer, and
buffer are classes.
A property is an associated descriptor which can be used to search or filter data. For example:
pH, autoscore=clear, acetate, and ammonium sulfate are properties.

© 2007–2012 Rigaku Automation, Inc. 1401718 Rev A
CHAPTER 1. INTRODUCTION
This manual provides operation and technical information for the Phoenix HT system and its
functions.
Also known as the Phoenix RE, the Phoenix HT (High Throughput) system is an enclosed station
in a CrystalMation system.
The Phoenix DT (Desktop) system is a standalone system.
1.1. General Description
The Phoenix HT system creates experimental plates using screens contained in deep-well blocks
and protein samples.
A dispense head containing 96 syringes draws specific volumes of chemicals from a deep-well
block and places them in a plate used for protein crystallization experiments (experimental
plate).
A single-channel nano-dispenser draws specific volumes of solution from sample vials and
dispenses them in experimental plates.
The Rigaku software interface acts as an executive for the Phoenix HT system; the Art Robbins
Instruments’Phoenix software can be accessed for maintenance purposes.
Figure 1. CrystalMation Phoenix HT

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© 2007–2012 Rigaku Automation, Inc. 2401718 Rev A
Figure 2. Phoenix Base System
A Phoenix HT system is part of a CrystalMation system.
Functions included with a CrystalMation Phoenix HT system are:
An enclosure to contain the entire system.
An Emergency Motor Off (EMO) button to stop the motors immediately in an emergency.
Start and Stop buttons.
An active nest, to precisely and automatically position an experimental plate.
An antistatic curtain, to reduce static electricity that can interfere with drop placement.
A protein chill block, to chill vials of protein or other substances.
Dual chimney wash station.
1.2. Phoenix HT System Major Components
The Phoenix HT instrument consists of a base Art Robbins’ system and additional components.
1.2.1 Phoenix Base System
Follow all safety cautions and warnings in “1.4. Potential Hazards” on page 9. For cabling and
electrical connections, see “Chapter 2. Installation” on page 10.
Figure 3. Phoenix Base System
96-Syringe
Dispense
Head
PlateDeck
P h o e n i x B a s e S y s t e m
Nano-Dispenser

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1.2.2 Enclosure Status Light Indicators
The status lights for the Phoenix HT instrument indicate the following conditions.
1.2.3 Protein Chiller Block
The protein chiller block uses a thermo-electric temperature controller to maintain a user-specified
temperature to prevent denaturation of protein samples. There are 16 temperature-controlled slots
and 2 slots that are not temperature-controlled, or ambient temperature. Each slot holds a 200 µl
PCR tube. The temperature is set using the interface on the thermo-electric control unit (Figure 3).
Figure 4. Protein Chiller Block
Color Standard Definition Machine Specific
All Off System has no power
Solid Red Power is on, software launched, software in
stopped state, or machine is not ready to process
orders. Machine can not start processing orders.
Stopped, not ready for plate to be
made.
Blinking Red Power is on, software launched, system has an
error condition and system has stopped, or the
system requires initialization, or the EMO is active.
Not initialized, EMO pressed,
liquid handling error.
Solid Amber Power is on, software launched, no errors but
supplies are low and system will run out and stop
soon, or the temperature is out of specification.
Supplies low.
Blinking Amber Power is on, software launched, no errors but
system has run out of supplies and stopped, or the
software is paused, or the doors are open or
unlocked.
Software paused, door open, low
water pressure.
Solid Green Power is on, software launched, no errors,
software is in idle state, waiting on orders. The
machine will automatically process orders when
they become available.
Idle, waiting on orders.
Blinking Green Power is on, software launched, no errors, system
is running, actively processing/moving.
Order being processed.
Blinking
Amber+Red
Power is on, software is not launched or control
system is not responding.
Application software not
connected.
Ambient temperature slots Temperature-controlled slots
1 2 3 4 5 6 7 8 . . . . . . 16 Slot Numbers

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© 2007–2012 Rigaku Automation, Inc. 4401718 Rev A
In the Phoenix HT enclosure, when accessing the the chiller block through the left-side access
window, the location numbers are in reverse order because the Phoenix system faces the
Integration Module.
Figure 5. Phoenix HT Chiller Block Slots
Figure 6. Temperature Controller Front Panel
Figure 7. Temperature Controller Rear Panel
To apply power to the Protein Chiller Block, flip the rocker switch on the back of the box labeled
Thermoelectric Temperature Controller underneath the deck.
To adjust the temperature, push and hold the SET button until the number on the display begins
flashing. Use the arrow keys to adjust the temperature setting. Push SET when the desired
setpoint is reached.
Always set to 7 V
Click to power ON.