TOPAZ™ FID Crystallizer
For Protein Crystallization
User Guide
P/N 68000007, Rev. A
September, 2004
Fluidigm Corporation and its suppliers own the written and other materials in the TOPAZ™ FID Crystallizer. The written materials are
copyrighted and protected by the copyright laws of the United States of America and, throughout the world, by the copyright laws of
each jurisdiction according to pertinent treaties and conventions. No part of this manual may be reproduced manually, electronically,
or in any other way without the written permission of Fluidigm Corporation.
Fluidigm® is a registered trademark of Fluidigm Corporation. MSL™ and TOPAZ™ are trademarks of Fluidigm Corporation. All of the
trademarks, service marks, and logos used in these materials are the property of Fluidigm Corporation or their respective owners.
You may not use, and nothing contained in these materials grants by implication, waiver, estoppel or otherwise, any right in any
trademark displayed in these materials without the written permission of Fluidigm Corporation or the respective owner.
NOTICE TO PURCHASER: For Research Use Only. Not for use in diagnostic procedures.
Patents pending.
Copyright 2002–2004 Fluidigm Corporation. All rights reserved.
Made in the USA
No right to modify, copy, use, or distribute TOPAZ FID Crystallizer software is provided except in
conjunction with the instrument delivered hereunder and only by the end user receiving such instrument.
NO WARRANTIES ARE PROVIDED, EXPRESSED OR IMPLIED. ALL WARRANTIES, INCLUDING THE
IMPLIED WARRANTIES OF FITNESS FOR PURPOSE, MERCHANTABILITY, AND NON-INFRINGMENT
ARE EXPRESSLY DISCLAIMED. By continuing the installation process, user agrees to these terms.
Please refer to the full text of the software license agreement supplied with the installation media for this
application.
Contacting Fluidigm
For Technical Support, send email to: [email protected]
Phone in United States: 1.866.FLUIDLINE (1.866.358.4354)
Outside the United States: 650.266.6100
On the Internet: www.fluidigm.com/support.htm
Fluidigm Corporation
7100 Shoreline Court
South San Francisco, CA 94080
CONTENTS
C ON T E N T S
1 Introducing the TOPAZ FID Crystallizer
Safe Use of the TOPAZ FID Crystallizer . . . . . . . . . . . . . . . . . . . . . . 1-1
Components of TOPAZ FID Crystallizer . . . . . . . . . . . . . . . . . . . . . . 1-4
Reagents and Chemicals . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-6
TOPAZ FID Crystallizer Basics . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-7
Dedicated Computer and Hand-held Barcode Reader . . . . . . . . . . 1-9
Care of the FID Crystallizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1-11
Care of Hand-held Barcode Reader . . . . . . . . . . . . . . . . . . . . . . . . . 1-12
2 Setting Up the FID Crystallizer
Site Requirements . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-1
Assembling the FID Crystallizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-5
Starting the FID Crystallizer . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-11
Supporting Chip Incubation at 4 ºC . . . . . . . . . . . . . . . . . . . . . . . . . . 2-13
User-Supplied Equipment . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2-14
3 Using FID Crystallizer Software
Features of FID Crystallizer Software . . . . . . . . . . . . . . . . . . . . . . . . . 3-1
Retrieving a Log for an Experiment Setup . . . . . . . . . . . . . . . . . . . . 3-14
A FID Crystallizer Verification
Using the TOPAZ Catalase Install Kit
B Recommended Specifications for Liquid Handling Robots
C Troubleshooting
Responding to an Error Message . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-3
Responding to a Power Failure . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . C-4
Installing FID Crystallizer software and Configuration Files . . . . . . C-6
D Technical Support
E Ordering Additional Parts
INDEX
Fluidigm Corporation, 2004
1
INTRODUCING
THE TOPAZ FID CRYSTALLIZER
Welcome to the TOPAZ FID Crystallizer, an automated system that
optimizes the screening of crystallization conditions and the growth of
high-quality crystals.This user guide walks you through:
•
Key features and benefits of the TOPAZ FID Crystallizer
•
Assembly of the hardware system that supports nanocrystallization
•
Confirmation of proper system function
Safe Use of the TOPAZ FID Crystallizer
Fluidigm uses the following user attention words in documentation. Each
denotes a message requiring a particular level of attention or action:
Note
Calls your attention to useful information.
IMPORTANT
Informs you of the correct usage of the system.
WARNING: LASER HAZARD! NOTIFIES YOU OF THE POTENTIAL FOR
SERIOUS PHYSICAL INJURY OR ILLNESS
THAT COULD OCCUR IF PRECAUTIONS ARE
NOT TAKEN.
IMPORTANT
Always wear the proper laboratory clothing—protective gloves,
lab coat, safety glasses—when handling any chemicals or any
TOPAZ Chips.
The TOPAZ FID Crystallizer is for research use only and is not for use in
diagnostic procedures.
1-1
Introducing the TOPAZ FID Crystallizer
Fluidigm Technical Support
Fluidigm Technical Support welcomes your questions or comments about
the usage and configuration of the TOPAZ FID Crystallizer. We are also
available to discuss crystal extraction methodologies, automation, and
strategies for optimizing crystallization. Contact Fluidigm Technical
Support by telephone or email. See Appendix D for more information.
Automating Crystallization While Enhancing Crystal Growth
The TOPAZ FID Crystallizer streamlines the process of setting up
crystallization experiments while conserving protein samples and enables
a more effective method for crystal discovery—free interface diffusion
(FID). FID may enable the growth of crystals where traditional methods
have failed.
Conventional methods for crystallizing proteins can be prohibitively
expensive in terms of time, labor, laboratory space, reagents, and sample
requirements. Robots alleviate the burden of conducting trials based on
vapor diffusion and economize on protein sample. However, robots may
not improve the rate of crystal discovery because vapor diffusion exposes
samples to a relatively small fraction of the reagent-protein
concentrations that may affect crystallization. In addition, robots are
difficult and expensive to maintain.
TOPAZ Technology for Crystallization
The fundamental technology that enables TOPAZ Chips is Fluidigm’s
MSL™ technology. Fluidigm uses MSL technology to fabricate
disposable microfluidic chips that can accurately and precisely meter
reagents and protein, eliminating hours of tedious manual pipetting.
Because the integrated fluidic circuit (IFC) on the TOPAZ Chip is made
from a gas permeable elastomer, extremely small amounts of protein and
reagents may be pressurized into its circuitry. This means you can
conduct experiments using nanogram quantities of protein—a dramatic
reduction compared to conventional methods. This savings provides the
flexibility to carry out studies of any protein, even one that is poorly
expressed.
1-2
Safe Use of the TOPAZ FID Crystallizer
The FID Crystallizer further expedites crystallization experiments by
letting you set up as many as four TOPAZ Chips simultaneously.
Software on a dedicated computer controls pressurization and valve
actuation on the FID Crystallizer to ensure precise, reproducible metering
of fluids.
The FID Crystallizer serves as a starting point for a fully computermediated process that supports every step of crystallization screening,
from experiment setup and incubation, to inspection and growth of
improved crystals.
1-3
Introducing the TOPAZ FID Crystallizer
Components of TOPAZ FID Crystallizer
2
1
3
TOPAZ FID Crystallizer, with TOPAZ Chips in the bays
and laptop mounted on the laptop shelf.
Figure 1
12
4
13
5
8
6
10
7
14
9
11
Figure 2
1-4
Components shipped with the TOPAZ FID Crystallizer
Components of TOPAZ FID Crystallizer
Table 1
Components Included in the TOPAZ FID Crystallizer (1 of 2)
#
Component
Purpose
Qty
1
FID Crystallizer
Controls filling of reagents and valve actuation in the
integrated fluidic circuits (IFCs) on up to 4 TOPAZ Chips at
a time.
1
2
Laptop computer,
mounted on laptop shelf
Runs FID Crystallizer software to control FID Crystallizer
functions, record barcode, experiment set up and data.
1 ea.
3
USB mouse
Mouse connects to laptop computer.
1
4
FID Crystallizer Software
CD
Installs FID Crystallizer software, configuration files and
pdf files for the FID Crystallizer.
1
5
Polyurethane Tubing,
Black, 1/8 in. ID,
1/4 in. OD
Connects source of high pressurized air to the FID
Crystallizer.
10 ft.
(~3.1 m)
Polyurethane Tubing,
clear, 1/8 in. ID,
1/4 in. OD
Connects source of low pressurized air to the FID
Crystallizer.
10 ft.
(~3.1 m)
6
Fitting, 1/4 MPT x 1/4 PTC
2 of each
7
Fitting, 1/4 FPT x 1/4 PTC
Used to connect source of compressed air to black and
clear polyurethane tubing.
8
Shut-off valve
Used to turn off gas supply to FID Crystallizer.
2
9
Tee, Instant Fit
Connects a single source of pressurized air (or nitrogen) to
two lengths of polyurethane tubing.
1
10
Quick disconnect fitting
Connects gas source to 1/4-in. OD polyurethane tubing
with the regulator.
2
11
1/4-20 x 1 1/2 socket head
screw, 1/4 washer, and
spacer
Affixes FID Crystallizer to bench, to stabilize for interaction
with robot.
3 of each
12
Pressure regulators,
100 psi & 40 psi,
connected by a porting
block with mounting
bracket.
Control the pressurized gas delivery to the FID Crystallizer.
1
13
12V Power Supply, with
country specific cord
Provides connection from FID Crystallizer to power source.
1
14
Barcode Reader
Supports scanning of barcode identifiers on TOPAZ Chips.
May be hand-held or mounted on stand.
1
Air Compressor, with
compressor filter kit
Alternate source of compressed air that has been validated
for operation with the FID Crystallizer. (not shown)
1
(Optional)
1-5
Introducing the TOPAZ FID Crystallizer
Table 1
#
Components Included in the TOPAZ FID Crystallizer (2 of 2)
Component
Purpose
Qty
Hydration Kit
Contains 1 bottle (10 mL) Hydration Fluid Concentrate and
PVA strips (not shown), for preparation of appropriate
humidity levels on the TOPAZ Chip during a crystallization
experiment. Store at room temperature.
1
TOPZ FID Crystallizer
Install Kit
Contains TOPAZ™ 1.96 Chips and reagents (not shown)
for validating the TOPAZ FID Crystallizer
1
OptiMix -1 Reagent Kit,
OptiMix -2 Reagent Kit,
OptiMix -3 Reagent Kit,
OptiMix -PEG Reagent Kit
Four 96-reagent screening kits (not shown), designed for
use with TOPAZ Chips.
Note: Refrigerate at 4 ºC upon receipt.
800 µL/
well
TOPAZ FID Crystallizer
User Guide
Describes in detail how to set up and use the
TOPAZ FID Crystallizer and the TOPAZ Install Kit. (not
shown)
1
To order additional items, contact Fluidigm Corporation at 1-866FLUIDLINE (1.866.358.4354).
Outside the United States, call 650-266-6100.
Reagents and Chemicals
The TOPAZ FID Crystallizer is shipped with the following chemicals in a
separate package:
•
30 µL of catalase in the TOPAZ Install Kit
•
One 96-reagent plate in the Install Kit
•
OptiMix -1 Reagent Kit, OptiMix -2 Reagent Kit, OptiMix -3
Reagent Kit, OptiMix -PEG Reagent Kit. Each kit contains
96 reagents that have been formulated for crystallization experiments
on TOPAZ Chips.
•
10 mL Hydration Fluid Concentrate
The first two chemicals are used in the crystallization of catalase,
described in Appendix A. Store these reagents and the OptiMix Reagent
Kits at 4 ºC with the lids tightly closed.
Store the Hydration Fluid Concentrate at room temperature with the lid
tightly closed.
1-6
TOPAZ FID Crystallizer Basics
TOPAZ Chip storage
To ensure the shelf life of the TOPAZ Chips:
•
Keep the TOPAZ Chip sealed in its packaging until you are ready to
use it.
•
Store TOPAZ Chips at room temperature and out of direct sunlight.
All TOPAZ™ Chips and the TOPAZ FID Crystallizer are intended for
research use only.
WARNING: CHEMICAL HAZARD! SOME OF THE CHEMICALS REFERRED TO IN THE USER GUIDE MAY
NOT HAVE BEEN PROVIDED WITH YOUR SYSTEM. PLEASE OBTAIN
AND REVIEW THE MATERIALS SAFETY DATA SHEETS (MSDS)
FROM THEIR MANUFACTURERS.
TO OBTAIN COPIES OF THE MSDS FOR CHEMICALS PROVIDED BY
FLUIDIGM, CALL THE FLUIDIGM CORPORATION AT 1-866FLUIDLINE (1-866-358-4354) OR OUTSIDE THE UNITED
STATES, CALL 650-266-6100.
TOPAZ FID Crystallizer Basics
Figure 3
The TOPAZ FID Crystallizer, with two TOPAZ Chips in bays
The TOPAZ FID Crystallizer and FID Crystallizer software controls the
pressure required to precisely meter fluids to the fluid channels and
control valves on the TOPAZ Chips at four bays. A hand-held barcode
reader attached to the dedicated computer supports sample tracking.
1-7
Introducing the TOPAZ FID Crystallizer
The FID Crystallizer
The FID Crystallizer automates chip run setup of TOPAZ Chips placed at
four front bays. Pressurized gas that feeds into the FID Crystallizer is
regulated at two different pressures: high pressure (85–100 psi) and low
pressure (32–60 psi). The high pressure is directed into a pneumatic
system that operates four moving arms on the front of the FID
Crystallizer. When activated, an arm drops down over the TOPAZ Chip
to form a seal. Low pressure gas is then directed through the arm and into
openings on the TOPAZ Chip to pressurize fluid and control channels.
When the FID Crystallizer is in use and the FID Crystallizer software is
open, all four arms are raised. When either the FID Crystallizer software
or the power on the back of the FID Crystallizer is turned off, an internal
shut-off valve checks the flow of pressurized gas. Over time, the arms
descend as pressurized gas to the arms decreases.
FID Crystallizer software installed on a dedicated computer runs scripts
for setting up experiments on up to four FID Crystallizers using
Fluidigm’s family of TOPAZ Chips and automates data collection for
each experiment.
An Adaptor Microplate can also be used with the
TOPAZ FID Crystallizer to pressurize fluid delivery on TOPAZ Chips
that are not compatible with SBS plate standards.
Operating environment
The FID Crystallizer should be used in an environment that meets the
requirements shown in Table 2 on page 8.
IMPORTANT
Table 2
1-8
The FID Crystallizer is for indoor use only!
Required Ambient Conditions
for FID Crystallizer Operation
Temperature
4 ºC – 30 ºC
Humidity
30 – 80%, non-condensing
Dedicated Computer and Hand-held Barcode Reader
Regulatory compliance
The Topaz FID Crystallizer meets with the European EMC Directives —
72/23/EEC, 89/336/EEC, 92/31/EEC, and 93/13/EC— and has been
tested to comply with the following standards:
•
EMC: EN 61326:1997, including Amendments 1:1998 and 2:2001,
Class B emissions limits
•
Safety: 61010-1:2001
Dedicated Computer and Hand-held Barcode Reader
The FID Crystallizer includes a laptop computer, keyboard, and mouse.
FID Crystallizer software controls the timing of valve actuation and
pressurization inside the FID Crystallizer. A hand-held barcode reader
attached to the computer supports sample tracking.
Laptop Computer
The computer features a 2.4-GHz P4 processor with 512 MB RAM, a 40GB hard drive, a graphics adaptor with 32 MB built-in RAM, a 1.44MB floppy drive, and a CD-RW/DVD-ROM combo drive. It runs on the
Windows® XP Professional operating system.
IMPORTANT
The computer supplied with the TOPAZ FID Crystallizer is
dedicated to running FID Crystallizer software. User-installed
software, especially programs that download and play music,
can compromise the performance of the FID Crystallizer
software. For optimum performance, only use the dedicated
computer to support the FID Crystallizer and sample tracking.
Scripts on the FID Crystallizer software control pressurization of control
channels and fluids at each step of the experiment setup. The FID
Crystallizer software maintains a log for every experiment setup that
includes the identity of the operator, the TOPAZ Chip, the script used,
and user comments. For details about FID Crystallizer software, see
Chapter 3.
1-9
Introducing the TOPAZ FID Crystallizer
Power options
Power options that are available with the Windows XP operating system
can interfere with FID Crystallizer software. On each dedicated laptop
computer that is shipped with the FID Crystallizer, the following power
options are set to Never:
•
System standby
•
System hibernate
IMPORTANT
Two power option settings—System standby and System
hibernate— must be set to ‘Never’ to assure reliable
performance of the TOPAZ FID Crystallizer!
•
You may adjust the ‘Turn off hard drive’ and ‘Turn monitor off’
settings without adversely affecting the performance of FID
Crystallizer software.
Barcode Labelling
Labels on the TOPAZ Chip contain the Fluidigm logo, a unique tencharacter number, and a one-dimensional, Code 128 barcode. With the
hand-held barcode reader provided, you can use this barcode to track
samples and experiments in a database.
If you choose to design your own barcode, the barcode reader can
accommodate the following 1D barcode formats: Code39, UPC/EAN,
Code128, Interleaved 2 of 5, RSS 14.
For compatibility with the Fluidigm database, the barcode should be
limited to 50 characters and should not contain the following characters:
\.,&[]{}/|*#()!@$%^:;
The barcode should not contain any of the first 31 ASCII characters, such
as:
1-10
ASCII
Symbol
ASCII
Symbol
0
nul
9
tab
10
newline
13
return
27
esc
Care of the FID Crystallizer
Care of the FID Crystallizer
The FID Crystallizer requires little maintenance beyond regular cleaning
of the bays and the gaskets in the moving arms. The gasket is the orange,
rubbery surface under the arm that comes in contact with the top of the
X.96 Chip. Clean the gaskets once a week, or whenever debris
accumulates on the gasket, or if the chip tends to stick to the gasket after
the arm is raised.
To clean the gaskets and bays
1
Quit FID Crystallizer software and then turn off the power to the FID
Crystallizer.
2
Lift each of the arms to gain access to the gasket—the surface that
touches the top of the chip.
3
With a clean, lint-free cloth and 70% isopropanol, carefully wipe the
gaskets and the surface of the bays.
IMPORTANT
Always turn off the power to the FID Crystallizer before cleaning
the gasket.
See Chapter 2 for information on:
•
Configuring the compressed gas input for TOPAZ FID Crystallizer
•
Equilibrating the TOPAZ FID Crystallizer at sub-ambient
temperatures
1-11
Introducing the TOPAZ FID Crystallizer
Care of Hand-held Barcode Reader
The clear plastic window inside the head of the barcode reader must be
kept clean for best performance. Avoid touching the plastic window.
WARNING: LASER HAZARD! CLASS 2 LASER BEAM.
DO NOT STARE INTO LASER!
If the window becomes dirty, clean it with a soft, non-abrasive cloth or
facial tissue that has been moistened with water. You may also use a mild
detergent to wash the plastic window; wipe the detergent off the window
with a damp cloth.
1-12
2
S E T T I N G U P T H E FID C R Y S T A L L I Z E R
This chapter describes:
•
Site requirements for operating the FID Crystallizer.
•
How to assemble the components of the FID Crystallizer. See page 25.
•
How to equilibrate the FID Crystallizer to cold room temperatures.
See page 2-13.
•
User-supplied equipment for monitoring crystal formation. See
page 2-14.
WARNING: LIFTING HAZARD! THE FID CRYSTALLIZER IS SHIPPED IN TWO CARDBOARD BOXES. THE
HEAVIER BOX CONTAINS THE CRYSTALLIZER AND WEIGHS 100 LBS.
(45 KG). THE SMALLER BOX WEIGHS 40 LBS (15 KG). USE CAUTION
WHEN MOVING THE SHIPPING BOXES.
Site Requirements
To operate the FID Crystallizer, your site requires:
•
Adequate electrical power
•
A source of clean, dry pressurized air or nitrogen
•
A workspace that accommodates the components
Electrical Requirements
Components of the FID Crystallizer, including the dedicated laptop
computer, should be plugged into a standard US-type power strip or surge
protector that provides single-phase AC voltage, between 100 and 240 (60
or 50 Hz). Current requirement is 5 amps, but the outlets must be of US
standard (NEMA 1-15P) blade type.
If you are not operating in the United States, Fluidigm provides a countryspecific 12V power supply with power cord.
2-1
Setting Up the FID Crystallizer
Uninterruptible power supplies
Power interruptions or outages can adversely affect experiment setup on
the FID Crystallizer, as described on page C-4.
If your local power supply is subject to frequent power interruptions, you
may protect your experiment setups on the FID Crystallizer by using an
uninterruptible power supply (UPS) with the minimum requirements
shown in
Table 3
UPS Minimum Requirements
to Run the FID Crystallizer
Output Power Capacity
500 W (800 VA)
Backup Time (Run-Time)
*30 minutes at 500 W
Output Voltage
100–120 VAC
Output Connection
NEMA 5-15R (at least 2 power outlets)
* A typical UPS requires battery packs to achieve 30 minutes backup time.
The UPS shown described in Table 3 is sufficient to maintain power to
one FID Crystallizer that is running without the aid of an air compressor.
If you plan to purchase the TOPAZ AutoInspeX Workstation, you
can protect both the FID Crystallizer and the AutoInspeX Workstation
with one UPS that has the minimum requirements shown in Table 4.
Table 4
UPS Minimum Requirements to Run Both the
FID Crystallizer and the AutoInspeX Workstation
Output Power Capacity
1000 W (1500 VA)
Backup Time (Run-Time)
*30 minutes at 1000 W
Output Voltage
100–120 VAC
Output Connection
NEMA 5-15R (at least 3 power outlets)
* A typical UPS requires battery packs to achieve 30 minutes backup time.
The UPS described in Table 4 is sufficient to maintain power to two
instruments: an FID Crystallizer that is running without the aid of an air
compressor and an TOPAZ AutoInspeX Workstation.
2-2
Site Requirements
Pressurized Gas
A consistent source of clean, dry, pressurized air or nitrogen is required to
supply the FID Crystallizer. The gas must be instrument quality (0.1micron filtered and dew point 20 ºC below ambient).
Two lines of pressurized gas feed the FID Crystallizer: high pressure (90–
100 psi) and low pressure (32–60 psi). Both lines may originate from a
single source of pressurized gas regulated between 90 and 100 psi. When
the regulator assembly supplied with the FID Crystallizer is attached to a
single source of pressurized gas, it provides two separate lines of
pressurized gas that are regulated to the required pressures.
As an alternative, each line may originate from a separate source of
pressurized gas: compressed air as the source of the high pressure gas
(85–100 psi) and compressed air or nitrogen as the source of the low
pressure gas (32–60 psi).
If house gas is not an option, you may purchase an air compressor that has
been validated for operation with the FID Crystallizer. Contact Fluidigm
Technical Support for details on ordering a validated compressor.
As a third option, a tank system may be used to provide pressurized gas.
With regular usage of the FID Crystallizer—one set of four TOPAZ
Chips per work day—a large cylinder of compressed gas [150 standard
cubic feet (scf)] lasts two weeks. With regular usage, a smaller cylinder
(80 scf) lasts one week. When FID Crystallizer software is not running or
power to the FID Crystallizer is turned off, a shut-off valve within the
FID Crystallizer stops the flow of pressurized gas. You may also use the
external shut-off valves to stop the flow of gas.
Air sources are connected to the FID Crystallizer with
¼-in. OD, semi-rigid polyurethane tubing. The output on the regulated
gas supply at the wall must be capable of connecting to either the
¼-in. OD semi-rigid polyurethane tubing or to a ¼-in. NPT(M or F)
fitting.
When using compressed gas cylinders, carefully monitor tank pressure
and replace cylinders before the tanks are completely empty.
2-3
Setting Up the FID Crystallizer
Note
Contact Fluidigm Technical Support to discuss validated compressors
and acceptable alternatives to pressurized air or nitrogen.
Work Space
Provide a work surface that can accommodate the FID Crystallizer and
dedicated laptop computer. Table 5 shows the dimensions and weights of
the components of the FID Crystallizer.
Table 5
Dimensions and Weights
of FID Crystallizer Components
Component
Length
in (cm)
Width
in (cm)
Height
in (cm)
Weight
lbs (kg)
FID Crystallizer
22 (56)
23 (58)
9 (23)
60 (27)
Dedicated laptop computer
11 (28)
13 (33)
13 (33)*
8.4 (3.8)
Hand-held barcode reader
3.3 (8.4)
2.5 (6.3)
6 (15.2)
0.3 (0.15)
* Height when laptop lid is open.
To accommodate these components, we recommend you supply a bench
top with a minimum depth of 25 in. (64 cm) and width of 23 in. (58 cm).
To allow adequate air circulation, keep an area at least 2 in. (5 cm) behind
the FID Crystallizer clear. To accommodate the laptop computer mounted
on a laptop shelf above the FID Crystallizer, provide at least 25 in. (64
cm) space above the bench top. If the laptop computer is not mounted
atop the FID Crystallizer, keep a space at least 6 in. (15 cm) above the
FID Crystallizer clear for circulation.
IMPORTANT
Do not place the FID Crystallizer on a heated surface or directly
above a source of heat.
Accommodating an air compressor
If you choose to use an air compressor that has been validated by
Fluidigm as the source of compressed air, provide adequate space for air
circulation around the compressor: at least 12 in (31 cm) behind the
compressor and at least 16 in (41 cm) above.
2-4
Assembling the FID Crystallizer
If you place the air compressor beneath the FID Crystallizer, the
FID Crystallizer must be sitting on a benchtop that is made of wood or
other non-heat conductive material and that is at least 1.5 in (4 cm) thick.
Provide adequate space for air circulation, as described in the preceding
paragraph.
Assembling the FID Crystallizer
Before you begin to assemble the FID Crystallizer, be sure you have all
the components listed in Table 1 on page 1-5. You will need a sharp blade
to cut the polyurethane tubing to the appropriate length for your site.
IMPORTANT
When the laptop computer is mounted on the provided shelf on
top of the FID Crystallizer, the computer must be grounded.
Grounding the laptop computer
A ground wire is provided to connect the rear of the computer to the
provided shelf. One end of the ground wire is attached to the provided
laptop shelf and ends with a banana plug. The other end of the ground
wire is attached to the laptop computer and ends with a banana jack. A
star washer is taped to the FID Crystallizer during shipment. Use this star
washer in conjunction with the laptop shelf to assure the laptop computer
is adequately grounded.
If the laptop computer is not mounted on the provided shelf, you do not
need to connect the two ends of the ground wire together.
To ground the computer mounted on the laptop shelf
1
Remove the star washer that is taped to the rear of the FID
Crystallizer during shipment.
A shiny, recessed surface on the baseplate at the rear of the FID
Crystallizer accommodates the star washer.
2
Place the star washer into the round recessed surface on the baseplate
of the FID Crystallizer.
3
Slip the lip of the laptop shelf over the baseplate and star washer.
2-5
Setting Up the FID Crystallizer
The hole in the shelf lip should line up with the holes in the star
washer and the baseplate.
4
Insert and tighten the 5/16-in socket head cap screw, shown in Figure
4, to secure the shelf to the baseplate and provide grounding for the
laptop shelf.
Make sure the computer and FID Crystallizer are located near a
power source that meets the site requirements.
5
Connect the banana plug and banana jack to complete the ground
wire connection.
USB Cable and Electric Connections
A universal serial bus (USB) port on the rear of the FID Crystallizer
accepts a cable that connects the FID Crystallizer to the dedicated
computer. The length of the provided USB cable is ~6 ft. (1.8 m).
USB cable output
Primary power switch
12 Vdc/5 A Jack input
5/16 in. socket head cap screw
in shelf and baseplate
Figure 4
Electronic ports and switches on the rear of the FID Crystallizer. The laptop
computer is shown mounted on the provided shelf.
IMPORTANT
Use the provided shelf to mount the laptop computer above the
FID Crystallizer. Do not place the laptop computer directly on
the top surface of the FID Crystallizer.
2-6
Assembling the FID Crystallizer
Connecting the USB cable to the computer
1
If the computer is not mounted on the provided shelf, place the
computer and the FID Crystallizer within 2 ft. (0.6 m) of each other
on the work surface.
Make sure the computer and FID Crystallizer are located near a
power source that meets the site requirements.
2
Connect the USB cable from the back of the FID Crystallizer to the
laptop computer. (See Figure 4.)
IMPORTANT
The addition of USB cable extensions to the provided system
may compromise voltage input. Do not add a USB extension
cable to the USB cable provided at the rear of the FID
Crystallizer.
Electrical Connections
Both the dedicated laptop computer and FID Crystallizer should be
plugged into a standard US-type power strip or surge protector that
provides single-phase AC voltage, between 100 and 240 VAC (60 or
50 Hz). Two country-specific 12V power supplies are shipped with the
FID Crystallizer: one for the laptop computer and one for the FID
Crystallizer. The 12V power supply for the laptop computer has a yellow
plug on one end.
To make power connections
1
Plug the round plug on the end of one 12V power supply cable into
the port labelled “12 Vdc 5.0 A” on the back of the FID Crystallizer.
See Figure 4 on page 2-6.
2
Plug the other end of the 12V power supply cable into the power strip
or surge protector.
3
Plug the yellow end of the second 12V power supply cable into the
laptop computer and the other end into the power strip or surge
protector.
Pneumatic Connections
For convenience, Fluidigm provides a regulator block which consists of a
high-pressure regulator and a filter connected by a porting block with
2-7
Setting Up the FID Crystallizer
mounting brackets to a low-pressure regulator. A length of 1/4-in OD
polyurethane tubing connects a source of clean, dry compressed air or
nitrogen to the regulator blocks and then to two inlets on the FID
Crystallizer. When one source of pressurized air feeds both inlets on the
FID Crystallizer, the source of pressurized gas should be regulated to
85 psi.
When a second source of pressurized air or nitrogen feeds the low
pressure gas port on the FID Crystallizer, the first source should be
regulated to 85 psi and the second source should be regulated to 40 psi.
All exterior air inlets on the FID Crystallizer and regulators are quick
disconnect fittings. When connecting tubing to a quick disconnect
fittings, push the tubing into the fitting as far as possible and then pull on
the tubing to verify the connection is tight and leak-proof.
Air: 85 psi
CDA/N2: 37-60 psi
Drain
Figure 5
Note
Pneumatic ports on the rear of the FID Crystallizer
To help distinguish between high and low pressure lines, connect black
polyurethane tubing to the source of high pressure and clear tubing to
the source of low pressure.
2-8
Assembling the FID Crystallizer
To connect one compressed air source to both inlets on the FID Crystallizer
1
Measure the distance from the source of compressed gas to the port
on the back of the FID Crystallizer that is labeled “Air 85 psi.”. (See
Figure 5 on page 2-8.)
Ten feet of black tubing is provided with the FID Crystallizer. If you
need to order additional tubing, see Appendix E.
2
Cut a piece of black polyurethane tubing to this length.
Cut perpendicular to the tubing length. Avoid cutting at an angle.
3
Attach one end of the tubing to the regulator on the gas source.
4
Push the other end into the port on the back of the FID Crystallizer
that is labeled “Air 85 psi.”
After pushing the tubing end into the port as far as possible, pull on
the tubing to make sure the connection is tight and leak-proof.
5
Determine a location for the regulator block somewhere along the
length of the polyurethane tubing and cut the tubing at this location.
The regulator block may be mounted on the wall or on the laptop
shelf.
6
Attach the black tubing coming from the source of compressed gas to
the input on the high-pressure regulator.
After pushing the tubing end into the port as far as possible, pull on
the tubing to make sure the connection is tight and leak-proof.
7
Attach the black tubing coming from the port on the FID Crystallizer
to the output on the high-pressure regulator. See Figure 6 on page 210.
8
Measure the distance from the second, low-pressure regulator to the
port on the back of the FID Crystallizer that is labeled “Air 32–
60 psi.”
9
Cut a piece of clear polyurethane tubing to this length.
10 Attach one end of the clear tubing to the low-pressure regulator outlet
on the regulator block.
11 Attach the other end of the clear tubing to the port on the back of the
FID Crystallizer that is labeled “Air 32–60 psi.” See Figure 6.
2-9
Setting Up the FID Crystallizer
Regulator Regulator
(100 psi) (60 psi)
CDA or N2
(85 psi)
Shut-off valve
(32–60 psi)
FID Crystallizer
Figure 6
One source of compressed gas with regulator block connected to two input
ports on the FID Crystallizer.
Connecting to two sources of compressed gas
When two sources of compressed gas feed the FID Crystallizer, one
source is regulated to 85 psi and feeds the high pressure port on the FID
Crystallizer; the second source of pressurized air or nitrogen should be
regulated to 40 psi and feeds the low pressure gas port on the FID
Crystallizer.
Note
To help distinguish between high and low pressure lines, connect black
polyurethane tubing to the source of high pressure and clear tubing to
the source of low pressure.
The block regulator that is shipped with the FID Crystallizer is configured
to support one source of compressed gas. If you prefer to use two sources
of compressed gas, you need a separate regulator for each gas source.
Contact Fluidigm Technical Support for assistance.
2-10
Starting the FID Crystallizer
Starting the FID Crystallizer
When you start up the FID Crystallizer, you have to turn on the
compressed gas and the electrical power. Your FID Crystallizer may have
either one or two sources of compressed gas.
To start up the FID Crystallizer
1
Open up the regulator (100 psi) at the source of compressed gas,
shown in Figure 6 on page 2-10.
2
Open the shut-off valve that is located at the regulator block.
If your system has two sources of compressed gas, open the regulator
after the high pressure regulator.
3
Confirm that the regulator is set to 85 psi.
If a second source of compressed gas is connected to the FID
Crystallizer:
4
a
Open the 40 psi regulator at the second source.
b
Open the shut-off valve located after the regulator
c
Confirm that the regulator is set to 40 psi.
Toggle the primary power switch to the ON (|) position.
The primary power switch is located at the rear of the FID
Crystallizer, as shown in Figure 4 on page 2-6.
5
Turn on the power to the dedicated computer.
FID Crystallizer software opens when the computer is turned on.
IMPORTANT
Always turn on the FID Crystallizer first, before turning on the
dedicated computer.
When turning off the system, first quit FID Crystallizer software,
then turn off the power to the FID Crystallizer.
Collecting Fluid Output
Depending on the purity of the pressurized gas system, condensate may
collect in the lines of the FID Crystallizer and escape through the drain on
the rear of the FID Crystallizer. (See Figure 5 on page 2-8.)
2-11
Setting Up the FID Crystallizer
•
Cut a short length—3 in (7.6 cm)—of the polyurethane tubing and
connect it to the drain on the rear of the FID Crystallizer.
Attaching the Hand-held Barcode Reader
The hand-held barcode reader is packaged with a USB cable and vendor
instructions that explain how to use the adapter to plug both the barcode
reader and the keyboard into the same port.
•
Follow the manufacturer’s instructions to attach the hand-held
barcode reader to the USB port on the laptop computer.
FID Crystallizer Software
One compact disk (CD) is shipped with the FID Crystallizer. It contains
Fluidigm’s FID Crystallizer software and the configuration information
for the FID Crystallizer.
2-12
Supporting Chip Incubation at 4 ºC
The FID Crystallizer software is pre-installed on the dedicated computer
before it is shipped to you. Use the CD to reinstall the FID Crystallizer
software and the configuration information, if one of the following events
happens:
•
The FID Crystallizer software is accidentally removed from the
computer
•
The hard drive on the dedicated computer has to be reformatted or
replaced
If you encounter any problems reinstalling the FID Crystallizer software
and configuration files, contact Fluidigm Technical Support. See page C6 for installation instructions.
Supporting Chip Incubation at 4 ºC
Scripts in FID Crystallizer software support loading and incubation of the
TOPAZ X.96 Chip at 4 °C with controlled free interface diffusion.
When you use these scripts at 4 °C, the FID Crystallizer must first be
equilibrated for at least 6 hours at the reduced temperature to minimize
the effects of condensation on moving parts.
To equilibrate the FID Crystallizer to a cold room
1
If the FID Crystallizer has been used at room temperature, turn it off.
2
Move the FID Crystallizer into the cold room and allow it to
equilibrate at 4 °C for at least 6 hr. before turning on the power.
To equilibrate the FID Crystallizer to room temperature
1
If the FID Crystallizer has been used in the cold room, turn it off.
2
Move the FID Crystallizer out of the cold room and allow it to
equilibrate at the room temperature for at least 6 hr. before turning on
the power.
2-13
Setting Up the FID Crystallizer
User-Supplied Equipment
To monitor crystal development, Fluidigm recommends the
TOPAZ™ AutoInspeX Workstation, a high-performance automated
detection system capable of interrogating every diffusion chamber in the
X.96 Chip. The AutoInspeX Workstation automates scanning
experiments on TOPAZ Chips for crystal development and growth, with
software that detects crystals, captures images, and stores data for further
analysis.
Lacking access to an AutoInspeX Workstation, you may use an inverted
optical microscope to manually scan the X.96 Chip.
Microscope
Use an inverted optical microscope to examine and monitor
crystallization on the X.96 Chip. In the inverted configuration, the
collected light must only travel through the substrate, approximately
1 mm. Convenient use with an upright microscope requires the collected
light to travel through 4-5 mm of elastomer. Thus the short working
distances required for high numerical aperture viewing are only possible
in the inverted configuration.
Regardless of the type of microscope being used, most crystals are readily
viewed in a brightfield transmitted light configuration, at 10X, without
using special imaging modes.
Note
Long or intense illumination may heat your sample and produce
undesirable results.
2-14
3
USING FID CRYSTALLIZER SOFTWARE
This chapter describes the features of the FID Crystallizer software,
including:
•
The Normal view, used for routine pressurization of TOPAZ Chips.
See page 3-5.
•
The Summary view, used for monitoring activity on multiple FID
Crystallizers. See page 3-11.
•
The Manual Mode tool. See page 3-12.
•
How to retrieve the software log for each script executed. See page 314.
Note
FID Crystallizer software is provided on a CD that is included in the
TOPAZ FID Crystallizer. See page C-6 for re-installation instructions.
IMPORTANT
Always turn on the FID Crystallizer first, before turning on the
dedicated computer.
When turning off the system, first quit FID Crystallizer software,
then turn off the power to the FID Crystallizer.
Features of FID Crystallizer Software
FID Crystallizer software has been pre-installed on the dedicated laptop
computer. The software controls the delivery of pressurized gas and the
timing of valve actuation on the FID Crystallizer. Scripts in the FID
Crystallizer software control pressurized fluid delivery throughout a
TOPAZ Chip run.
Tool Icons
A row of icons under the menu bar (Figure 7 on page 3-2) are links to
tools.
3-1
Using FID Crystallizer Software
•
Click an icon to open the associated view or tool.
Normal View
Help
Summary View
Script Editor
Manual Mode
Figure 7
Open Log
Icons below the menu bar provide links to additional views and tools
Normal View. Normal view is the screen that appears when FID
Crystallizer software opens. See page 3-5 for more information.
Summary View. This screen displays an overview of the status of all
scripts running. See page 3-11 for more information.
Script Editor. A separate application that provides tools for writing and
editing scripts. This application is not included in the standard software
package.
Manual Mode. This screen lets you manipulate the arms and adjust
pressurization. See page 3-12 for more information.
Open Log. Open Log lets you retrieve logs of the activity associated with
each chip. See page 3-14 for more information.
Help. Online help provides detailed information about the commands and
screens available in FID Crystallizer software.
Scripts for Delivering Pressurized Gas
Scripts control a specific sequence of chip loading and valve actuation
activities, such as those shown in Table 6 on page 3-3. Each script
comprises one or more steps. Typically, one step signals a change in
pressure at one or more channels on the TOPAZ Chip.
Overview of scripts used
Scripts are available to support chip runs for each TOPAZ Chip that has
been designed. New scripts are developed with each new TOPAZ Chip
3-2
Features of FID Crystallizer Software
that is tested and released. The specific pressurization activities that
scripts control can be grouped into four categories. All scripts incorporate
one or more of the script categories shown in Table 6.
Table 6
Five Categories of Scripts
Script Category
Purpose
Prepping
Activate control valves.
Loading
Blindfill of reagent and protein into respective
chambers.
Initiating diffusion
Closes containment valves and open interface
valves.
Ending diffusion
Terminate FID.
Recharging
Maintain pressure to both accumulators.
For more specific information about scripts for any chip, refer to the user
guide for that chip.
Pausing scripts
FID Crystallizer software provides two different methods for temporarily
stopping a script, or pausing. The first pause method is available in all
scripts; the second pause method is only available in the 5 Auto... scripts.
When a script is in a pause, you can raise the arm and gain access to the
chip, if necessary, to load protein or inspect channels and valves.
During a pause, while the arm is down and covering the chip, delivery of
pressurized gas continues. You can use this feature to extend pressurized
loading of reagents and protein.
Pauses in all scripts. After any script has started, a Pause button becomes
available. After you click Pause, you can inspect the chip or introduce
reagents and protein into the chip inlets. You can also choose to stop the
script altogether by clicking Abort. See page 3-4.
Pauses in 5 Auto... scripts. In addition to the pause described above,
while a 5 Auto script is running, when the chip is ready for a particular
task, a software message appears that begins with “Pause...”. When you
3-3
Using FID Crystallizer Software
click OK in the message, you have 10 seconds to click Pause at the
appropriate bay. If you do not click Pause, the script continues after 10
seconds.
The Pause in the 5 Auto script gives you time to add reagent or protein to
the chip inlets or to inspect chamber volumes. Once you have completed
these tasks, replace the chip in the bay, engage the arm and resume the
script.
Aborting scripts
After you click Pause during a script, the Abort button becomes available.
When you click Abort, the script is terminated at the step that was in
progress when you clicked Pause. The valve states and accumulator
pressures in the chip are determined by the action taken during the
interrupted step.
Support for Up to Four FID Crystallizers
Up to four FID Crystallizers can be connected to one laptop running FID
Crystallizer software. An icon for each FID Crystallizer appears at the top
of the Normal view, shown in Figure 8 on page 3-5.
3-4
•
Click an FID Crystallizer icon to set up experiments and monitor
script progress on that FID Crystallizer.
•
Right-click an FID Crystallizer icon to change the name associated
with that FID Crystallizer.
Features of FID Crystallizer Software
FID
Crystallizers
Graphic
representation
of step activity
Progress bars
Control buttons
Run information
and user comments
Indicator icons change color
to indicate pressurizing
Figure 8
Use the Normal View of FID Crystallizer software to execute scripts at all
four bays and on up to four FID Crystallizers.
The Normal View in FID Crystallizer software
Use the Normal view to run the scripts that control pressurization of
accumulators and fluid delivery in TOPAZ Chip. This section describes
the features of the Normal view that you can use for experiment setup.
Four Bay Setup positions
When FID Crystallizer software opens, the Normal view displays four
Bay Setup positions associated with the selected FID Crystallizer. At each
Bay Setup, scripts control pressurization of channels in a TOPAZ Chip.
Each Bay Setup in the FID Crystallizer software provides fields where
you enter information to uniquely identify the experiment.
•
Chip ID. Use the barcode reader to scan the chip barcode or type in a
chip identifier.
3-5
Using FID Crystallizer Software
•
Experiment. Enter the name of the experiment associated with the
chip.
When you click Start to begin running a script, FID Crystallizer
software links the Experiment name to the Chip ID. After they are
linked, the Experiment field is automatically populated when you
enter the Chip ID in a bay setup.
•
Operator. Select a name from the drop-down menu or enter a new
operator name.
•
Script. Select a script from the drop-down menu.
To enter a new Operator name
1
Click the Operator drop-down menu and select Add Operator.
2
Enter a name in the Operator dialog box.
Running a script
•
After you have entered information in all the Bay Setup fields, click
Start.
Before the script starts running, the arm in the bay descends onto the
chip. See page 3-9 for descriptions of the control buttons available
while a script is running.
You may click Pause while a script is running. During a pause, delivery of
pressurized gas continues as long as the arm in the bay is seated on top of
the TOPAZ Chip. See page 3-9.
When the script is complete, Finish becomes active and pressurized gas
delivery stops.
•
When you click Finish, the arm at the bay raises to allow access to the
TOPAZ Chip.
Note
To conserve compressed gas, when no scripts are running at any of the
four FID Crystallizer bay positions and the mouse attached to the
dedicated computer is not moved, the shut-off valve inside the FID
Crystallizer automatically closes after one minute.
3-6
Features of FID Crystallizer Software
Group Mode
Group Mode is a feature that lets you run the same script simultaneously
in two or more Bay Setups. If you use any control buttons—Pause, Abort,
Resume, Raise Arm, or Lower Arm— in one bay when a script is running
in Group Mode, the action also occurs at all of the other bays that are
running in Group Mode.
Group Mode checkbox
Figure 9
Group Mode is a feature of Bay Setup
To use Group Mode
1
Place prepared TOPAZ Chips in two or more bays.
2
Click the Group Mode check box in the Bay Setups associated with
the chips placed in Step 1.
3
Enter Chip ID and Experiment name for each Bay Setup included in
Group Mode.
4
Enter Operator and Script in one Bay Setup included in Group Mode.
All Bay Setups in Group Mode automatically use the same Operator
and Script.
5
Click Start at one Bay Setup.
All Bay Setups in Group Mode start and run simultaneously.
Also see “Advanced Options” on page 11 for an alternative to Group
Mode that does not require entering Chip ID or Operator name at each
Bay Setup.
3-7
Using FID Crystallizer Software
Graphic of step activity
Scripts in the FID Crystallizer software contain steps. Pressurization
changes at each step are represented by a graphic at each bay position.
Protein chambers are shown in blue, reagent chambers in yellow. Vertical
lines across the top and bottom of the graphic represent containment
channels, while the vertical line between the chambers represent the
interface channel.
Red Xs indicate a pressurized channel (closed valve), while red circles
represent pressure release (an open valve). See Figure 10.
Graphic representation
of step activity
Step progress bar
Overall progress bar
A green check mark and
the Finish button indicate the
script is completed.
Figure 10
Two bay positions showing script activity.
Progress bars
When a script is running at a Bay Setup, two progress bars appear. (See
Figure 10.) The top progress bar reports on the total time and time
remaining in each step in the script. The bottom progress bar reports on
the total time and time remaining in the entire script.
3-8
Features of FID Crystallizer Software
Control buttons
Control buttons, located below the progress bars, allow you to manage
scripts and, during a pause, to raise and lower the arm at each bay. You
can use them to Start, Finish, Pause, Abort, or Resume a script.
•
Click Start to begin running a script.
The arm in the bay descends as the script begins.
Pause and Add Comments become active after you click Start.
•
Click Pause to freeze the progress bar activity without stopping
pressurized gas delivery. See page 3-3.
•
See page 3-10 for a description of Add Comments.
When you Pause a script, Abort, Resume, and Raise Arm become active.
•
Click Abort to terminate the script.See page 3-4.
•
Click Resume to continue the script and progress bar activity.
•
Click Raise Arm to gain access to the TOPAZ™ Chip in the bay.
When you raise the arm, pressurized gas delivery stops.
After you click Raise Arm, Engage Arm becomes active.
•
Click Engage Arm to continue pressurized gas delivery to the
TOPAZ Chip in the bay. The progress bar activity continues when
you click Resume.
A large green check mark indicates that the last step of a script is
completed. At the end of a script, Finish becomes active and pressurized
gas delivery stops. An accumulator that is pressurized at the end of a
script maintains control valve closures for up to 7 days, or until its check
valve is depressed–either manually or by running a script.
•
When you click Finish, the arm in the bay raises to allow access to the
TOPAZ Chip in that bay.
3-9
Using FID Crystallizer Software
Add Comments
After you click Start, Add Comments becomes active.
•
Click Add Comments to open the Comments dialog box.
Comments appear in the Information field and in the experiment log.
See page 3-14 for more information about the log.
When you click Finish, Add Comments becomes inactive.
Information about the run
While a script is running, the Information field displays the data entered
during setup—Chip Barcode, Experiment, Operator, Script—and the date
and time the script began running. If you add comments, the comments
also appear in the Information field.
Indicator icons
Icons at the bottom of each Bay Setup in the FID Crystallizer software
change color as the FID Crystallizer pressurizes channels. Table 7 lists
the colors associated with each channel being pressurized. An additional
icon changes color when a TOPAZ Chip is in position at a bay.
When the FID Crystallizer applies pressure to a channel, or when the
TOPAZ Chip is positioned correctly in the bay, the appropriate icon
displays the color shown in Table 7. When the pressure is released, the
corresponding icon turns gray.
Table 7
Icon
Icons in FID Crystallizer Software
On Color
Indicates
Magenta
Yellow
On Color
Indicates
TOPAZ Chip
positioned
correctly in bay
White
Pressure on
to reagent
channels
Pressure on
to interface
Green
Pressure on
to containment
channels
Blue
3-10
Pressure on to
protein channel
Icon
channels
Features of FID Crystallizer Software
Advanced Options
With Advanced Options, as in Group Mode, you can run the same script
simultaneously at all Bay Setups. In addition, the following identifiers are
applied in Advanced Options:
•
The Barcode ID field is automatically populated by a number 1
through 4.
•
The Experiment field is populated by “Experiment Bay” plus the Bay
number.
•
The Operator field is populated by “Lab.”
To apply Advanced Options
1
In Normal view, choose Tools> Advanced Options.
The Advanced Options dialog box appears.
2
Click On to apply Advanced Options to the next chip run on the FID
Crystallizer.
Advanced Options is applied to all subsequent runs unless you either
turn off and restart FID Crystallizer software or turn off Advanced
Options.
Using the Summary View
In the Summary View, you can monitor activity at all Bay Setups on up to
four FID Crystallizers running simultaneously. Summary View displays:
Operator, Script Running, Overall Progress bar, Time Remaining until the
script ends, and the indicator icons.
3-11
Using FID Crystallizer Software
Figure 11
The Summary View displays the status of all scripts running on up to four
FID Crystallizers.
To open the Summary View
•
In the View menu, choose Summary View.
As an alternative, click the Summary View icon at the top of the
screen.
Using Manual Mode
With the Manual Mode tool, you can move the arms at each bay, apply
pressure to specific channels, and open check valves. Typically, Manual
Mode is used by Fluidigm Technical Support and is not for daily
operation of the FID Crystallizer.
IMPORTANT
The FID Crystallizer can be seriously damaged if the pressure
set in Manual Mode falls outside the pressure range supplied
through the gas regulators. Always verify that pressurized gas
feed is turned on and adequate before using Manual Mode.
3-12
Features of FID Crystallizer Software
Figure 12
The Manual Mode tool
IMPORTANT
Finish all scripts that are running in Normal view before using
the Manual Mode tool.
To open Manual Mode
•
In the Tools menu, choose Manual Mode.
As an alternative, click the Manual Mode icon at the top of the screen.
IMPORTANT
Use Manual Mode only for brief checks of system function.
Click Done to return to Normal view as soon as possible. Do not
leave the FID Crystallizer unattended while using Manual
Mode.
3-13
Using FID Crystallizer Software
Retrieving a Log for an Experiment Setup
FID Crystallizer software creates a log of each experiment you setup on
the FID Crystallizer. Each log is a tab-delimited file that you can export
as an *.txt file. Use the Query Log to search for a particular log by one or
more of the following parameters:
• Chip ID
• Script
• Operator
• Experiment
• Run Time–the first day in a range
• To–the last day in a range of days
Figure 13
The Query Log dialog box
To query for log files
1
Choose File > Open Log...
2
Choose one or more parameters from the pull-down menus in the
Query Log dialog box.
3
Click Search Query to retrieve log files that contain the query
parameters.
Note
To search for all runs performed on one specific day, enter the date that
precedes the specific day in the Run Time field and enter the specific day
in the To field.
3-14
Retrieving a Log for an Experiment Setup
To export a log file
•
Highlight one or more logs in the query results and click Export.
To open an exported log file
1
Use Microsoft Excel to open the *.txt log file.
2
In the Text Import Wizard, choose Delimited file type with Tab
delimiters.
When the log file opens in Excel, the Begin Time column may show
###### instead of the time and date. To see the time and date
expressed as numbers, select the column and stretch it to at least
91 pixels.
Columns in exported log file
When exported, columns in the tab-delimited log file are labeled: Chip
ID, Experiment, Run ID, Step, Step Name, Begin Time, Message,
Comments.
Run ID. FID Crystallizer software counts every time you click Start at
the beginning of a script. The number in the Run ID column is a tally of
the number of times a script has been started on all FID Crystallizers.
Message. FID Crystallizer software writes a message to the log when the
following events occur: Script Begins, Step Begins, Pause Experiment,
Resume, Script Ends, Finish, Terminated (written when you click Abort).
3-15
Using FID Crystallizer Software
3-16
A
FID CRYSTALLIZER VERIFICATION
USING THE TOPAZ CATALASE INSTALL KIT
Use the TOPAZ Catalase Install Kit to confirm proper FID Crystallizer
function and setup. Run the Install Kit when you first receive the
FID Crystallizer and as necessary for troubleshooting.
TOPAZ Catalase Install Kit
The Install Kit contains:
•
One vial of catalase (30 µL)
•
A 96-well reagent block of positive and negative controls
Store the reagents and protein at 4 ºC with the lids tightly closed. Prior to
use, centrifuge the reagent block for 2–5 min. at 1000 x g.
Thaw the catalase solution, if frozen, before using. Centrifuge the tube in
a mini-centrifuge, 1 min. at 10,000–13,000 xg, to pellet aggregates, if any.
Avoid disturbing the pellet when pipetting the protein solution.
Standard Protocol for Catalase Crystallization
Before beginning the validation, assemble the FID Crystallizer, as
described on page 2-5. Review the critical timing requirements, shown in
Table A-1 on page A-2.
A-1
Table A-1
Steps with Critical Timing Requirements
Step
Perform...
See...
Add diluted Hydration Fluid to the chip and
reseat lid.
immediately after package is opened
page A-2
Activate control valves and dispense reagents.
within 20 hr. after adding diluted Hydration
Fluid
page A-3
Dispense protein to chip
within 60 min. after reagent dispensing
page A-5
Blind fill (pressurize delivery of reagent and
protein).
within 5 min. after protein dispensing
page A-5
Perform T0 scan (optional)
within 60 min. after loading script is
finished
page A-5
Run 3 FID Control RT
within 60 min. after T0 scan
page A-6
IMPORTANT
Do not place labels on the top or the bottom of the 1.96 Chip
where they may hinder the seal between the chip and the
gasket on the bay. You may place a label on the side of the
chip, but it should lay flush and should not fold over onto the top
of the chip or onto the protruding flange at the bottom.
To prepare the TOPAZ 1.96 Chip
IMPORTANT
Before you open the chip packaging, prepare sufficient volume
of diluted Hydration Fluid to deliver to the PVA strips.
1
Use sterile D.I. water to prepare a solution of 2 parts water and 1 part
Hydration Fluid Concentrate.
Each 1.96 Chip requires 1.5 mL of diluted Hydration Fluid. Prepare
enough diluted Hydration Fluid for all the chips you will use in a day.
A-2
2
Remove the 1.96 Chip from its packaging and raise the lid that covers
the hydration chamber.
3
Immediately add 750 µL Hydration Fluid solution to each strip of
PVA in the hydration chamber moats.
Fluidigm Corporation, 2004
Note
Make sure the PVA strips lie in the outer reservoirs, away from the
central integrated fluidic circuit (IFC). Do not allow diluted Hydration
Fluid to make contact with the IFC.
4
Immediately replace the hydration chamber lid and press the corners
of the lid firmly into place.
The lid should be flat and the edges of the lid should be completely
seated within the walls of the hydration chamber. The PVA strips
absorb the liquid within minutes.
Note
To maintain humidity, keep the lid on the hydration chamber
throughout chip run and chip scanning.
IMPORTANT
Charge the hydrated chip and dispense reagents within 20 hr.
of adding diluted Hydration Fluid to the hydration chamber.
Activating the Control Valves
After you introduce diluted Hydration Fluid into the 1.96 Chip, run the
1 Prep script.
To activate control valves
1
2
In the FID Crystallizer software, enter the chip and chip run
information at a bay position.
•
Scan or enter the chip Barcode.
•
Enter Experiment name.
•
Enter the Operator name
•
Select the 1 Prep script.
Place the hydrated 1.96 Chip on the corresponding FID Crystallizer
controller bay.
Align the notched corner of the chip with the A1 label in the bay.
3
Press Start.
As the script begins, the arm drops down to cover the 1.96 Chip.
4
Fluidigm Corporation, 2004
When the script is completed, click Finish.
A-3
After control valves are closed, you can pipette the reagents and protein
into the 1.96 Chip.
IMPORTANT
Reagents must be dispensed within 20 hr. of closing control
valves. Protein must be dispensed within 60 min. of reagent
dispensing.
Introducing Reagents and Protein into the 1.96 Chip
IMPORTANT
When pipetting manually, make sure there are no air bubbles in
the pipette tip. Pipette to the center and bottom of each inlet.
Press down only to the first pipettor stop to avoid introducing air
into the bottom of the inlet.
When using a liquid-dispensing robot, set the height of the pipette tips
as close as possible to the bottom of each reagent inlet to minimize
the formation of air bubbles. Ensure that all tips are levelled at the
bottom of the well. When pipetting viscous reagents, allow sufficient
time for complete delivery.
IMPORTANT
Reagents and protein delivery must be pressurized within
5 min. of protein dispensing.
Protein dispensing guidelines
When pipetting microliter amounts of protein, take the following
precautions to assure adequate delivery of protein into the protein inlet:
A-4
•
Use a well-calibrated, low-volume pipettor.
•
Make sure there are no air bubbles in the pipette tip.
•
Pipette directly to the center of the bottom of the protein inlet. Avoid
pipetting to the inlet sides.
•
Depress plunger to the first stop and wait one second before removing
the tip.
•
After removing the pipette tip from the inlet, verify that the tip is
empty and that protein has been delivered into the inlet.
Fluidigm Corporation, 2004
To pipette the catalase crystallization reagents and protein
1
Pipette 10 µL of each reagent from the 96-well reagent block into the
appropriate reagent inlets on the 1.96 Chip.
Refer to the TOPAZ™ 1.96 Chip User Guide for details on the
numbering system for reagent inlets.
2
Pipette 1.4 µL of catalase into the protein inlet on the 1.96 Chip.
To pressurize reagent and protein blindfill
1
In the FID Crystallizer software, select the appropriate Bay position,
then enter the chip barcode, select the operator name, and select the
2 Load 1.96 script.
The barcode number is linked to the Experiment name that was
entered when you ran the 1 Prep script.
2
Click Start to pressurize reagent blind fill into chambers.
3
When the script is finished, click Finish.
At the end of the 2 Load 1.96 script, all reagent and protein wells are
filled. If some wells are not filled, see page C-1.
At this point, you can perform a Tzero (T0) scan.
IMPORTANT
Perform a T0 scan within 60 min. of completing the 2 Load
1.96 script. Initiate diffusion within 2 hr. of completing the 2
Load 1.96 script.
Scan at T0
The TOPAZ™ AutoInspeX Workstation automates scanning and
detection of crystals in all the wells on a 1.96 Chip. The Image
Acquisition software performs a scan of all 96 diffusion chambers in less
than 5 min., saves images of all the diffusion chambers, and designates
the initial scan of the 1.96 Chip as T0. Auto Processor software requires a
T0 scan to process subsequent chip scans. After the T0 scan, initiate
diffusion.
If you do not have access to the TOPAZ AutoInspeX Workstation, you do
not need to perform a T0 scan.
Fluidigm Corporation, 2004
A-5
IMPORTANT
Initiate diffusion within 60 min. of completing the T0 scan.
Initiating Controlled FID
The 3 FID Control RT script releases pressure at the interface
accumulator to open the interface valves and initiate diffusion. The chip
remains on the FID Crystallizer for sixty minutes of equilibration, after
which time the interface valve is closed to interrupt diffusion.
To initiate diffusion
•
Run the 3 FID Control RT script after T0.
At the end of the 3 FID Control RT script, incubate the chip.
Monitoring Crystal Formation
For the catalase validation protocol, repeat the chip scan at 24 hr. after T0.
To monitor crystallization
1
After the T0 scan, scan again at 24 hr.
2
Score each well, recording crystal formation and clear wells.
Results
Catalase crystals typically form within 24 hr. Crystals form in at least 46–
48 (95%) of the diffusion chambers with positive control within 24 hr.
Crystals are not found in wells with negative control. Table A-2 on
page A-7 shows the locations of catalase crystals in blue.
A-6
Fluidigm Corporation, 2004
Table A-2
Locations of Crystals (blue cells)
in Validation Experiment
Cell
A1
A2
A3
A4
A5
A6
A7
A8
A9
A10
A11
A12
Fluidigm Corporation, 2004
1
2
3
7
8
9
13
14
15
19
20
21
25
26
27
31
32
33
37
38
39
6
5
4
12
11
10
18
17
16
24
23
22
30
29
28
36
35
34
42
41
40
43
44
45
50
49
55
51
57
56
62
61
67
63
69
68
74
73
79
75
81
80
86
85
91
48
47
46
53
54
60
52
58
59
65
66
72
64
70
71
77
78
84
76
82
83
89
90
96
87
93
92
88
94
95
Cell
B1
B2
B3
B4
B5
B6
B7
B8
B9
B10
B11
B12
A-7
A-8
Fluidigm Corporation, 2004
B
RECOMMENDED SPECIFICATIONS FOR
LIQUID HANDLING ROBOTS
Lateral positioning accuracy
+/- 1 mm
Vertical positioning accuracy
+/- 200 µm, including the vertical stage position error and
the relative flatness between the robot arm and the robot
workbench.
Syringe pump volume
Reagent pipetting: 500 µL or less
Protein pipetting: 250 µL or less
Pipette tip / Arm configuration
To pipette to protein wells, the robot may use a single tip
arm.
To pipette to reagent wells, an 8-tip arm configuration is
more suitable for aspirating from a 96-well reagent block
and then dispensing into the 384-well plate spacing of
TOPAZ screening chips.
Tip diameter
All recommended specifications assume a tip with 1.1 mm
outer diameter and 0.5 mm inner diameter. Tips of larger or
smaller diameters may work with modified system
parameters.
Dispensing volume
Reagent wells: 10-20 µL
Protein wells: at least 1.4 µL
Lateral well dispensing position
The center of the well.
Vertical well dispensing position
200 µm above the bottom of the well.
Liquid flow rates
Aspirating: 4 µL/s. Dispensing: 5 µL/s
Tip retraction
Avoid retracting the tips while dispensing to minimize bubble
formation.
Well locations and spacing
Wells on the TOPAZ x.96 chips are located and spaced
according to SBS standards for 384-well plate designs. The
chip layout provides 96 wells out of the 384 wells possible.
Well bottoms
Reagent well bottoms are flat
Protein wells bottoms are conical
IMPORTANT
Take special care to ensure that air bubbles do not obstruct the
opening at the bottom of each reagent well. Pay special
attention to the vertical dispensing position accuracy, as
described above. Bubbles severely extend the time required to
load reagents and proteins.
B-1
B-2
C
TROUBLESHOOTING
Observation
Possible Cause
Recommended Action
At the end of a script,
the appropriate
valves are not
closed.
Obstacle prevents proper seal
between chip and arm.
•
Check that the chip is seated and flat on the
bay, with the notch in the chip aligned to the
A1 on the bay.
•
Make sure the hydration chamber lid is flat
and firmly seated on the chip.
•
Check that the surface of the chip is flat and
free of cracks.
Some chambers in
the TOPAZ Chip are
not filled at the end
of a Load script.
Protein was not loaded before
running the script.
To dispense and load protein into wells:
a. Dispense protein into the protein inlet.
b. Place the chip on the bay and run
the Reload script.
Reagent was not dispensed to
one or more reagent inlets.
To dispense and load reagent into wells:
a. Determine which reagent inlet was not filled.
b. Dispense reagent to the missed inlet.
c. Place the chip on the bay and run the
Reload script.
Hand-held barcode
reader does not read
barcodes.
Error Message:
Warning: High
pressure for
Controller 1 does not
meet requirements.
Air bubbles in reagent channel.
•
Place the chip on the bay and run
the Reload script.
Dirty plastic window on reader.
•
Wipe the window with a soft, non-abrasive
cloth or tissue that has been moistened with
water. If necessary, use a mild detergent to
clean the window, then wipe off the
detergent with a dampened soft cloth.
Barcode reader not connected
to laptop.
•
Connect the cable from the barcode reader
to the USB port on the laptop computer.
Supply of pressurized gas is off
or low.
•
Make sure the source of compressed gas is
turned on.
•
Make sure polyurethane tubing, 1/4 in. OD,
is firmly connected to the port on the rear of
the FID Crystallizer and to the source of
pressurized gas.
•
Make sure the shut-off valve plumbed into
the polyurethane tubing is open.
•
See “Responding to an Error Message” on
page C-3.
C-1
Observation
Possible Cause
Recommended Action
Error Message:
Warning: High
pressure for
Controller 1 does not
meet requirements.
Leak in Polyurethane tubing,
1/4 in. OD.
•
Call Fluidigm Technical Support
at 1-866 Fluidline (1-866-358-4354).
•
Check that the 12 V power supply is
plugged into the FID Crystallizer and into
the AC power source.
•
Make sure the primary power switch on the
rear of the FID Crystallizer is turned on.
•
Make sure the dedicated USB cable at the
rear of the FID Crystallizer is connected to
the computer.
•
Remove any USB cable extensions that
have been added to the provided USB
cable.
TOPAZ Chip or Adaptor
Microplate not seated correctly
in bay.
•
Make sure the chip or the Adaptor
Microplate lies flat and is positioned
correctly. The notched corner should align
with the A1 label on the bay.
An obstruction is preventing the
arm from descending
completely.
•
Check the surface of the arm gasket and
remove any obstructions.
•
If the arm cannot be moved:
Leak inside FID Crystallizer.
Hardware failure
Error Message:
There is no controller
installed.
Error Message:
Failed to create
empty document.
Error Message:
Arm cannot engage.
Power to the FID Crystallizer is
turned off.
FID Crystallizer is not connected
to the computer
a. Quit the FID Crystallizer software.
b. Restart the software program to reset
system status.
Error Message:
Unable to process
command interface
pressure.
Supply of pressurized gas is off
or low.
Hardware failure
C-2
•
Make sure the source of compressed gas is
turned on.
•
Make sure polyurethane tubing, 1/4 in. OD,
is firmly connected to the port on the rear of
the FID Crystallizer and to the source of
pressurized gas.
•
Make sure the shut-off valve that is plumbed
into the polyurethane tubing is open.
•
See “Responding to an Error Message” on
page C-3
•
Call Fluidigm Technical Support
at 1-866 Fluidline (1-866-358-4354).
Observation
Possible Cause
Recommended Action
The FID Crystallizer
software quits
unexpectedly.
Communication between the
FID Crystallizer and FID
Crystallizer software has been
disrupted.
a. Check that both ends of the USB cable that
connects the FID Crystallizer to the laptop
are firmly attached.
b. Check that the 12 V power supply is
plugged into the FID Crystallizer and into
the AC power source.
c. Restart the FID Crystallizer software.
Power options in operating
system have been modified.
•
On the laptop computer, go to Settings >
Control Panel > Power Options. Make sure
the following two options are set to ‘Never’:
System standby; System hibernate.
Responding to an Error Message
When the FID Crystallizer software reports an error message, it might
indicate one of the following:
•
A missing connection between the FID Crystallizer and the dedicated
computer, or the FID Crystallizer is not turned on
•
Insufficient pressurized gas supply to the FID Crystallizer
•
A component failure within the FID Crystallizer
Figure C-1 An example of an error message in FID Crystallizer software.
What Actions to Take
When an error message appears on your computer screen, you can take
corrective action to eliminate the cause of the error message and then
proceed with the chip run setup or you can terminate the setup. The
troubleshooting table on page C-1 lists possible error messages and
descriptions of corrective actions.
Refer to the troubleshooting table on page C-1 for a description of the
appropriate corrective actions to perform.
C-3
•
If the error interrupted a script, review “Responding to a Power
Failure” on page C-4.
•
If the error message indicates a malfunction that requires attention
from Fluidigm Technical Support, stop the FID Crystallizer software
and contact Fluidigm Technical Support.
How An Error Message Condition Affects Your Chip Run Setup
Depending on what stage of the process you have completed, some error
messages alert you to a condition that could affect your chip run setup in
the same way as a power failure. Table C-1 lists the error messages, the
condition that might cause that message, and which steps in the chip run
setup might be affected.
Table C-1
Effects of Error Message Condition on Chip Run Setup
Error Message
Caused by
Affected Step in Process
There is no controller
installed.
Power to FID Crystallizer off or
disconnected.
•
Pressurizing the protein and
reagent channels
Failed to create empty
document.
Cable between FID Crystallizer
and dedicated computer loose
or disconnected.
•
Closing the containment channels
•
Priming control channels
•
Pressurizing the protein and
reagent channels
High pressure for Controller
does not meet requirements.
Unable to process command
interface pressure.
Insufficient gas source.
Regulator on gas source set too
low.
See “Responding to a Power Failure”
on page C-4.
Leak in polyurethane tubing.
Leak inside FID Crystallizer.
Responding to a Power Failure
If a power failure occurs while you are setting up a chip run on the
FID Crystallizer, the FID Crystallizer shuts down. The FID Crystallizer
software saves a log of the steps that occurred before the power outage.
To retrieve a log file, see page 3-13.
When power returns, you will have to restart the FID Crystallizer
software and rerun the script for each chip run in the bays.
C-4
Note
If your area is subject to frequent power outages, you may use an
uninterruptible power supply (UPS) to minimize disruption to your chip
run setups. See page 2-1 for minimum requirements.
Possible Scenarios
When a power outage occurs, its effects on your chip run setup vary,
depending on what stage of the process you have just accomplished. The
four steps in the chip run setup most likely to be affected by a power
outage are:
•
Activating the control valves (running 1 Prep script)
•
Pressurizing the reagent or protein blindfill
•
Opening the interface valves to initiate diffusion
•
Closing the interface valves to control FID
Activating the control valves
If the control valves are being activated when a power failure occurs, the
control valves may not be closed and the accumulators may not be
charged. Control valves must be closed before you load reagents and
protein. When the power returns, rerun the 1 Prep script to activate
control valves.
Loading reagent or protein
If you have already pipetted reagents or protein and have begun running a
Load script when a power failure occurs, pressurized blindfill subsides.
Accumulator pressure maintains pressure of control valves for seven
days.
When the power returns:
1
Restart FID Crystallizer software and re-enter the chip run identifiers.
2
Restart the 2 Load script.
C-5
Opening the interface valves to initiate diffusion
If a power failure occurs during a script that opens the interface valve to
initiate diffusion, the interface valves may not be open. If the interface
valves are not open, diffusion does not begin.
When the power returns:
1
Restart FID Crystallizer software and re-enter the chip run identifiers.
2
Run any of the ‘3 FID...’ scripts to initiate diffusion.If you use 3 FID
Start, run the 7 Recharge script after the appropriate equilibration
time to close the interface valves and terminate FID.
Closing the interface valves to terminate FID
If a power failure occurs during a script that closes the interface valve to
terminate FID, the interface valves may not be closed. If the interface
valves remain open, diffusion continues and FID is not terminated within
the recommended equilibration time. As a result, the concentration of
protein in the protein chamber may continue to decrease.
The effect of extended equilibration on the outcome of your
crystallization screens cannot be predicted.
When the power returns:
1
Record the precise equilibration time.
This time will be useful for designing future translation experiments.
2
Restart FID Crystallizer software and re-enter the chip run identifiers.
3
Run the 7 Recharge script to close the interface valves and terminate
FID.
Contact Fluidigm Technical Support for further evaluation.
Installing FID Crystallizer software and Configuration Files
One CD is included with the components shipped with the
FID Crystallizer. It contains FID Crystallizer software and four
configuration files for the FID Crystallizer.
C-6
The contents of this CD are pre-installed on the dedicated laptop
computer before it is shipped with the FID Crystallizer. If the hard disk on
the laptop is erased, you must reinstall the FID Crystallizer software and
all four configuration files.
Configuration files
The names of the calibration files begin with the words
“FCIIIConfigFileSN...” and end with three unique digits. The installation
process puts the configuration files into the Bin folder found at:
C:\Programs\Fluidigm\FIDCrystallizer\Bin.
Note
You do not need to have Administrative access to the computer to install
FID Crystallizer software.
To reinstall FID Crystallizer software
1
Insert the CD that contains the FID Crystallizer software into the CD/
DVD drive on the laptop computer.
An installation wizard presents an installation dialog.
Figure C-2 The installation dialog box for FID Crystallizer software
2
Click Install FID Crystallizer and follow the install instructions.
The InstallShield© Wizard program searches the hard drive for older
versions of the FID Crystallizer software. When it finds an older
version, a dialog box asks you if you want to remove the old version.
C-7
3
Click OK to remove the old version.
After it remove the old version, the installation dialog box shown in
Figure C-2 on page C-7 reappears.
4
Click Install FID Crystallizer and follow the install instructions.
5
When installation is complete, click Finish to stop the install wizard.
To read Help files, you must also install Adobe Acrobat Reader.
C-8
D
TECHNICAL SUPPORT
Fluidigm Technical Support is available to assist you at any stage of the
protein crystallization process, from screen to beam. This can include
questions about Fluidigm products, planning and setting up experiments,
inspections, extractions, and troubleshooting. Fluidigm Technical Support
can be contacted by telephone or email.
telephone (United States): 1-866-FLUIDLINE (1.866.358.4354)
telephone (outside the U.S.) 650-266-6100
email: [email protected]
Internet: www.fluidigm.com/support.htm
address: 7100 Shoreline Ct.; South San Francisco, CA 94080
D-1
D-2
E
ORDERING ADDITIONAL PARTS
Contact Fluidigm Corporation at 1-866-FLUIDLINE (358-4354) to order
any of these additional items. Outside the U.S., call 650-266-6100.
Fluidigm
Part Number
Item Description
Supplier
TPZ-M-4.96
TOPAZ 4.96 Chip (96 reagent, 4 protein)
Fluidigm
TPZ-M-1.96
TOPAZ 1.96 Chip (96 reagent)
Fluidigm
81000025
Hydration Fluid Concentrate, 10 mL
Fluidigm
TPZ-R-OS1
OptiMix -1 Crystal Screening Reagents, 96
Fluidigm
TPZ-R-OS2
OptiMix- 2 Crystal Screening Reagents, 96
Fluidigm
TPZ-R-OS3
OptiMix -3 Crystal Screening Reagents, 96
Fluidigm
TPZ-R-OSPE
OptiMix-PEG Crystal Screening Reagents, 96
Fluidigm
TPZ-AIX
TOPAZ AutoInspeX Workstation
Fluidigm
TPZ-FID
TOPAZ FID Crystallizer Assembly
Fluidigm
TPZ-FID-A
TOPAZ FID Crystallizer Assembly with validated air
compressor
Fluidigm
42000002
FID Crystallizer software
Fluidigm
68000007
TOPAZ™ FID Crystallizer User Guide
Fluidigm
68000018
Quick Reference Card, Features of 1.96 Chip
Fluidigm
68000041
Quick Reference Card, Features of 4.96 Chip
Fluidigm
91000012
Shut-off Valve Assembly, 2 (1/8" fNPT),
2 (1/8" mNPT to 1/4" OD Quick Disconnect)
Fluidigm
91000113
Regulator assembly
Fluidigm
61000051
Carrier Hotel, with cap screw and lock nut
Fluidigm
91000108
Adaptor Microplate
Fluidigm
72000062
Polyurethane tubing, 1/4" OD, 10 ft. (3 m), black
Fluidigm
72000119
Polyurethane tubing, 1/4" OD, 10 ft. (3 m), clear
Fluidigm
91000110
Bench mount hardware
Fluidigm
Supplier Part
Number
E-1
Fluidigm
Part Number
Item Description
Supplier
72000132
Pneumatic Porting Block, 1/4 NPT, 72 Series
Fluidigm
72000133
Pneumatic Quickclamp & Wall Mount, 72 Series
Fluidigm
72000035
Tee, barbed fitting, 1/8 in. ID
Bay Advanced
Technology
59000057
Hand-held barcode scanner (1D), with USB cable
and hands-free stand.
Symbol
59000021
Power Supply, 12 V, 5 A
CUI, Inc.
DTS120500UCP5-ET
91000122
*JUN-AIR® Air Compressor
Pacific Air
Technology
1609060
*Compressor Filter Kit
Supplier Part
Number
T3(1/8 B3)
LS2208
-7AZU0300S
PAC400-OF302
72000022
Tubing, Tygon Micro-Bore,
0.020 in. ID x 0.060 in. OD
VWR
63018-044
72000030
Gel Loading Pipette Tip
VWR
37001-152
*Compressor with filter has been validated by Fluidigm for use with the TOPAZ FID Crystallizer.
E-2
CONFIDENTIAL
INDEX
INDEX
A
P
aborting a script 3-4
advanced options 3-11
air compressor 2-4
pausing a script 3-3, 3-9
pipetting manually A-4
power failure recovery C-4
power option settings 1-10
power supply
12V 2-1
uninterruptible 2-2
B
barcode reader, care of 1-12
C
configuration files, installation C-6
R
E
raising arm 3-9
reagent, pipetting viscous A-4
regulatory compliance 1-9
robot, liquid handling B-1
engaging arm 3-9
equilibrating the FID Crystallizer 2-13
error messages C-1, C-2
F
FID Crystallizer components 1-4
FID Crystallizer software 3-1
installation C-6
G
gas supply, pressurized 2-3
ground wire 2-5
Group Mode 3-7
H
hydration chamber lid A-3
I
S
site requirements 2-1
software CD C-6
T
Table
components in FID Crystallizer 1-5
dimensions and weights of components 2-4
icons in software 3-10
Technical Support D-1
TOPAZ AutoInspeX Workstation 2-14
troubleshooting C-1
U
installing software C-6
uninterruptible power supply 2-2
USB cable 2-7
L
V
log files 3-14
M
validation protocol A-1
voltage requirements 2-1
microscope requirements 2-14
MSL™ technology 1-2
O
ordering parts E-1
INDEX-1
INDEX
INDEX-2