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Rigaku Phoenix HT User Manual

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Phoenix HT
TM
User Manual
May 2012
401718 Rev A

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Summary of Contents for Rigaku Phoenix HT

  • Page 1 Phoenix HT User Manual May 2012 401718 Rev A...
  • Page 2 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.

  • Page 3: Table Of Contents

    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.
  • Page 4 Phoenix HT User Manual 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...

  • Page 5: Preface

    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. 401718 Rev A...
  • Page 6 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. © 2007–2011 Rigaku Automation, Inc. 401718 Rev A...

  • Page 7: 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.

  • Page 8: Phoenix Ht System Major Components

    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.

  • Page 9: Enclosure Status Light Indicators

    Phoenix HT User Manual 1.2.2 Enclosure Status Light Indicators The status lights for the Phoenix HT instrument indicate the following conditions. Color Standard Definition Machine Specific All Off System has no power Solid Red Power is on, software launched, software in...
  • Page 10 Phoenix HT User Manual 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.

  • Page 11: Wash Stations

    Phoenix HT User Manual 1.2.4 Wash Stations The 96-head wash station and the nano wash station are supplied with wash water from the water pump control box. The pump control box controls the flow of the wash water. Water enters the controller from the water pump control box, and is pumped through one line to the nano-wash station, and through two lines to the 96-head wash station.

  • Page 12: Nano-Dispense Controller

    Phoenix HT User Manual The 96-head wash station has 96 channels, one for each needle in the 96-dispenser head, to increase wash efficiency and eliminate cross contamination. The wash station is mounted on the deck in Slot 8. Nano wash station...

  • Page 13: Anti-Static Bar

    Phoenix HT User Manual Cable to power supply adapter Nano trigger connection to Phoenix base system rear panel USB cable to computer Figure 12. Nano-Dispense Controller, Rear 1.2.6 Anti-Static Bar The anti-static bar removes static electricity from crystallization plates before use. Static electricity can cause the dispense drops to shift inside the subwells.

  • Page 14: Plate And Shelf Sensors

    Phoenix HT User Manual 1.2.8 Plate and Shelf Sensors A sensor bar over the shelves holds the plate sensors and the shelf sensors. The shelf sensors determine whether the upper or lower shelf is in the sensing position. Plate sensors determine whether a plate is present in a specific position on a shelf.

  • Page 15: Potential Hazards

    The control computer is connected via Ethernet to the Database Server. 1.4.2 Electric Power Hazards The Phoenix HT system operates using 100-240 VAC. Keep any moisture or foreign objects out of the enclosures. Do not apply power to the equipment in wet environments or when moisture may have entered the equipment.
  • Page 16 If the system fails, note what happened, any messages that appear on the monitor, lamp displays, what the system was doing before the failure, and any steps that were taken to correct the problem. Then contact the Rigaku Automation Service Department for assistance. © 2007–2012 Rigaku Automation, Inc.

  • Page 17: Chapter 2. Basics

    CHAPTER 2. BASICS This chapter contains instructions for setting up, starting and shutting down the system. The Phoenix HT system creates experimental plates using screens contained in deep-well blocks and protein samples. The 96-syringe dispense head is used to transfer an 8x12 array of solutions simultaneously.

  • Page 18: Shutting Down The System

    Follow the operating procedures current in your laboratory setting. Refer to the guidelines and instructions in the original-equipment Phoenix Setup Guide, in “Chapter 3. Quick Start Procedures” on page 14, and in the “Chapter 4. Phoenix HT Application Reference” on page 19 of this manual. 2.4.

  • Page 19: Using The Stop, Start, And Emergency Stop (Emo) Pushbuttons

    2.5. Using the Stop, Start, and Emergency Stop (EMO) Pushbuttons Located on the Phoenix HT enclosure, the Start, Stop, and EMO pushbuttons are used as follows: Immediately shuts off power to the Phoenix HT instrument, stops movement, and stops the Art Robbins Phoenix application.

  • Page 20: Chapter 3. Quick Start Procedures

    Phoenix system . 3.1. Preliminary Setup Open the left-hand access door of the Phoenix HT enclosure and manually insert the sample tubes into the protein chiller block. Accessing the chiller block...

  • Page 21: Phoenix Ht Software Procedures

    Batch Load in CrystalTrak NOTE: The detailed protocol for the Phoenix HT is created independently by Rigaku, and is not created using the Art Robbins’ Phoenix application. The protocol used on the Phoenix HT system is installed on the Phoenix HT laptop application prior to delivery, and is automatically used by the Phoenix system.
  • Page 22 Phoenix HT User Manual To register the sample(s) on the deck, click the Register Samples button in the lower right-hand corner of the window and click OK when a message to register additives appears. For each sample of the three samples in this example job, select the appropriate entry for each field, then click OK.
  • Page 23 (dead) volume. NOTE: Depending on the nano dispenser provided with your Phoenix, the liquid classes may vary or additional ones may be added. Consult your Rigaku Service representative for the latest liquid classes available. Verify that all protein samples have been added.
  • Page 24 Phoenix HT User Manual Add sufficient volume to the tube in the Edit Kalypso Chilled Sample dialog box and click Be sure to physically increase the sample volume in the sample tube to match the edited volume in the software.

  • Page 25: Chapter 4. Phoenix Ht Application Reference

    CHAPTER 4. PHOENIX HT APPLICATION REFERENCE The Phoenix HT system is controlled by Phoenix HT software. This chapter describes the operator interface with the following topics: “Organization” on page 19 “File Menu” on page 20 “View Menu” on page 20 “Jobs Menu”...

  • Page 26: File Menu

    Phoenix HT User Manual 4.2. File Menu The File menu contains the command to Exit the application. You may also exit the application by clicking the red button with the white X in the upper right of the window. 4.3.

  • Page 27: Tools Menu

    Figure 6. Tools Menu Poll Phoenix Status: Displays the status of the Phoenix HT in the system message area. Poll I/O Status ...: Displays the status of the Phoenix HT inputs and outputs in the system message area. © 2007–2012 Rigaku Automation, Inc.
  • Page 28 Phoenix HT User Manual Machine Control ...: Displays the Machine Control dialog to move the top and bottom trays. Click the Position box to show the menu. Choose the Forward, Middle or Back position from the menu and click the Move button to move the tray.

  • Page 29: Help Menu

    Figure 11. Options Dialog 4.6. Help Menu The Help menu contains the About ... selection to display the version number of the Phoenix HT application and other data. 4.7. Views Pane and Icons The buttons in the navigation panel display the views: the list of jobs with the Jobs button, the devices with the Manage Devices button, and previous jobs with the Job History button.

  • Page 30: Manage Device View

    Phoenix HT User Manual Figure 12. Jobs View 4.9. Manage Device View The Manage Device view displays the solutions in the chilled blocks and ambient blocks of the protein chiller, and the plates currently assigned on the shelves. 4.9.1 Chilled Block and Ambient Block Tabs The Chilled Block tab and the Ambient Block tabs display the samples in the chilled block and the ambient block.

  • Page 31: Onboard Plates Tab

    Clear All: Removes all samples in the list. 4.9.2 Onboard Plates Tab The Onboard Plates tab displays the plates currently on the shelves in the Phoenix HT base system. Barcodes that start with Z identify source blocks. The CrystalMation system loads up to two crystallization plates.

  • Page 32: Job History View

    Phoenix HT User Manual Figure 16. Manage Devices View, Onboard Plates Tab The active buttons on the right are: Edit: Opens the Edit Onboard Plate dialog, which allows you to edit the plate barcode. Figure 17. Edit Onboard Plate Dialog Remove: Removes the selected plates.
  • Page 33 Phoenix HT User Manual The menu and buttons on the right are: Show History For: Opens a menu for the time period of the jobs listed. Details: Opens a Details pane to show details of the selected job. Add to Jobs: Opens a dialog to add a job to the list.

  • Page 34: Chapter 5. Maintenance

    This extensive process is an option in Rigaku Service Contracts. 5.2. Equipment Cleaning Use a gentle nonabrasive detergent to clean surfaces of the Phoenix HT instrument. If a spill occurs on the equipment, stop the current exterior process and immediately remove all foreign matter.
  • Page 35 Phoenix HT User Manual (1) Set the number of times to loop through the steps. (2) Set the aspirate and dispense from the detergent cleaner in the chiller block Tray 10. Figure 1. Cleaning: Aspirate and Dispense Detergent Three Times The aspirate and dispense steps (the detergent wash) can be configured in this manner.

  • Page 36: Replacing The Nano-Tip Valve Harness Assembly

    Phoenix HT User Manual 5.4. Replacing the Nano-Tip Valve Harness Assembly Replace the nano-tip if it starts to drip or becomes clogged or damaged. 5.4.1 Removing the Nano-Tip Valve Harness Shut down all Phoenix components: Click the Disconnect button on the Phoenix toolbar to disconnect the motors. The button label changes to Connect.
  • Page 37 Phoenix HT User Manual Remove the velcro strap (if present) and the P-clamp that holds the harness in place on the nano head. Remove the P-clamp on the back of the Phoenix system that also holds the harness in place.
  • Page 38 Phoenix HT User Manual Twist and disconnect the pneumatic tubing from the nano dispense controller. Twist and disconnect the pneumatic tubing. Carefully disconnect the nanotrigger wire from the needle tip by pulling on the white connector which also holds the nano-tip in place and remove the nano-tip from the nano-tip sleeve.

  • Page 39: Installing The Replacement Nano Valve Harness

    Phoenix HT User Manual 5.4.2 Installing the Replacement Nano Valve Harness Replacing the nano valve harness includes installing the new harness and updating the software calibration file. To install the new nano valve harness: Connect the new pneumatic tubing to nano dispenser controller.
  • Page 40 Check that all connections and tubing is tight. Turn on the power for the nano controller box and the Phoenix HT instrument. Re-establish the software connection with the instrument by selecting Connect on the Phoenix software. Do a protocol test run to confirm that all parts are full operational.

  • Page 41: Calibrating The Nano Dispenser

    Phoenix HT User Manual Observe that the vacuum pump runs for a short time, then stops. If it runs continuously, remove and reinstall the new tip. If the vacuum pump is working properly, obtain one sample tube filled with water and gently submerge the nano-tip in it.
  • Page 42 Phoenix HT User Manual Click the Connect button in the Engine Control section. The dialogue appears as the instrument homes all motors. Always WAIT until the instrument has fully completed a requested command and the software correctly displays the outcome.

  • Page 43: Aligning The Nano Dispenser

    Phoenix HT User Manual When centered, click the Update XY Tray Position. button 10. Click the Save button. 11. Click the Stop Teaching button. 12. Click the Save and Close button. 13. Repeat steps 13 through 24 for the remaining tray positions.
  • Page 44 Phoenix HT User Manual Adjust the jog increment to the desired resolution using the pulldown box at the bottom of the page, then jog the X and Y axes the distance estimated in step 3. Keep in mind that the shelves will need to move in the opposite direction.

  • Page 45: Options And Spare Parts

    APPENDIX A. OPTIONS AND SPARE PARTS The following options and spare parts list is current as of the date of publication. Contact the Rigaku Automation Service organization for updated information. Table 3. Phoenix Options and Spare Parts Part # Description...

  • Page 46: Facilities Layout And Cabling

    The following sections display physical and electrical layout considerations for the Phoenix HT. B.1. Mechanical Layout The following information is current as of the date of publication. Contact the Rigaku Automation Service organization for updated information. Bracketed dimensions are in inches. Unbracketed dimensions are in millimeters.
  • Page 47 Phoenix HT User Manual Figure 45. Power and Network Connections The following figures are components installed in the Phoenix HT enclosure. Top View Front View Figure 46. Phoenix Base System Front and Top Dimensions and Weight © 2007–2012 Rigaku Automation, Inc.
  • Page 48 Phoenix HT User Manual Figure 47. Phoenix Side (Depth) Dimensions and Power Requirements Figure 48. PC Power Requirements © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...
  • Page 49 Phoenix HT User Manual Top View Side View Figure 49. Temperature Controller Unit Dimensions and Power Requirements Top View Side View Figure 50. Nano-Dispense Controller Dimensions and Power Requirements © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...
  • Page 50 The following connections must be taken to properly set up the system. This does not need to be repeated unless the equipment has been disconnected. Connect the cables to the Facilities Panels of the Phoenix HT base system, the temperature control, the pneumatic control, the control computer, and the wash system as shown.
  • Page 51 Do not disconnect electrical connections to house at arrow (rear panel of base system) water Waste-water lines connected to underside of Phoenix Supply Tank Waste-Water Tank Figure 52. Phoenix HT Electrical Cable Connections © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...
  • Page 52 Phoenix HT User Manual Water supply (Plumbed) Phoenix water connections (underside of base system) Water Control Module Waste water (Plumbed) Figure 53. Phoenix HT Water Connections © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...
  • Page 53 Peltier Chill Block FU-5 Anti-Static 0.5 A Bar Power Supply FU-7 FU-6 1.6 A 1.6 A DC Power 24 V Supply FU-8 3.15 A Figure 54. Phoenix HT Enclosure Power and Fuse Specifications © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...

  • Page 54: Revision History

    Part Number: 401718 Rev A Effective Date Revision Description of change 05/30/12 Complete rework of and update to Phoenix RE user manual DOO1457 published in 2008, separated into Phoenix HT User Manual and Phoenix DT Supplement manual. APPROVAL BLOCK TITLE NAME SIGNATURE...

  • Page 55: Index

    Filter Job Display part names hanging drop performing plate inventory hardware parts physical layout hazards plate definitions in CrystalTrak Help menu plate inventory plates, approved for Phoenix HT Poll I/O Status © 2007–2012 Rigaku Automation, Inc. 401718 Rev A...
  • Page 56 Phoenix HT User Manual sample protein Poll Phoenix Status scope of this manual positioning plates sensor bar positioning sample tubes sensors, plate and shelf power requirements Service and Support base unit and PC setup, initial nano-dispense controller shutting down the system...

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