Clarity Getting Started Clarity ENG Code/Rev.: M006/50B Date: 11. 9. 2013 Phone: +420 251 013 400 Fax: +420 251 013 401 clarity@dataapex.com www.dataapex.com DataApex Ltd.
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Getting Started Table of Contents Contents 1 Brief Description 1.1 Hardware and software requirements 2 Installation 2.1 Multilingual Clarity 2.2 Software Installation 2.2.1 Windows Vista installation 2.3 Hardware Installation 2.3.1 Hardware key (dongle) installation 2.3.2 The INT9 Card 2.3.3 Installation of the Colibrick Converter 2.4 Device setup and wiring 2.4.1 Standard cable for the Clarity station 2.4.2 Chromatograph 2.4.3 Autosampler 2.5 Clarity Configuration 3 Qualification procedures 3.
Table of Contents Clarity 7.2.5 DEMO (in the window header) 7.2.6 User accounts file load error 7.3 Problems upon collection of data 7.3.1 Data Acquisition - non-functional 7.3.2 Data Acquisition - Simulated 7.3.3 Other Error Messages 7.4 Hardware Key 7.4.1 Rockey USB dongle (re)installation 7.4.2 Rockey LPT dongle (re)installation 7.4.3 Sentinel dongle installation 7.5 System Files (systeminfo.txt file) 7.6 Sleep Mode 7.
Getting Started Table of Contents To facilitate the orientation in the Getting Started manual and Clarity chromatography station, different fonts are used throughout the manual. Meanings of these fonts are: Instrument (blue text) marks the name of the window, to which the text refers. Open File (italics) describes the commands and names of fields in Clarity, parameters that can be entered into them or a window or dialog name (when you already are in the topic describing the window).
Getting Started 1 Brief Description 1 Brief Description Clarity chromatography station is an effective tool for the acquisition, processing and evaluation of data from any gas or liquid chromatograph with analog output and from selected chromatographs with digital output. In the maximum configuration, it is possible to measure on up to four chromatographs simultaneously, from which, each may be equipped with up to 16 detectors.
Getting Started 2 Installation 2 Installation Verify that the package is complete (packing list). Caution: Install Clarity before inserting any devices (INT9, U-PAD2, Colibrick, etc.). 2.1 Multilingual Clarity From version 5.0 the Clarity software is supplied with multiple language support. Software is available in several languages including English, Spanish , French , Russian and Chinese .
2 Installation Clarity Note: If you are only evaluating the program, do not enter the User Code and press the Skip button. l During installation of the drivers on Windows XP the following message may appear: "The software has not passed Windows Logo testing". If this occurs, select "Continue Anyway". The drivers will be installed according to the list of components selected in the Choose Component window at the beginning of the installation.
Getting Started 2 Installation 2.3 Hardware Installation The following chapters describe the installation of a protective Hardware key (dongle) and the brief installation of the most common integration converters INT9, U-PAD2 and Colibrick. Caution: Plug in the USB devices ( ROCKEY USB hard lock, Colibrick or UPAD2) only after the installation of the Clarity station. A detailed description of the hardware and its installation, including troubleshooting, is available in separate manuals. 2.3.
2 Installation Clarity 2.3.2 The INT9 Card In Windows 8/7/Vista/XP the drivers will be installed automatically during the installation of Clarity. l Install the Clarity software first. Caution: l l l l Installing Clarity before inserting any devices (INT9, Colibrick, U-PAD2, etc.) is vital for the correct function of any A/D Converter! Turn off the PC. Insert the INT9 card into the PCI slot. Start up the PC.
Getting Started 2 Installation 2.4 Device setup and wiring The wiring strongly depends on the particular station. Clarity station packages which use an A/D converter (e.g. Colibrick) include a cable set composed of signal, starting and digital output for connecting the Clarity station to the chromatograph. Using directly controlled detectors skips the necessity of having an A/D converter - in such case continue in the chapter "Clarity Configuration" on pg 9. 2.4.
2 Installation Clarity 2.4.2 Chromatograph Connect cables according to one of the diagrams in Fig 4 on pg 7. Use a symmetrical connection only if you are sure that the chromatograph/detector is equipped with a symmetrical output - it is necessary to read through the instructions for the corresponding chromatograph. Fig 4: Connection of a Clarity station with a chromatograph All current DataApex A/D Converters INT7, INT9, U-PAD, U-PAD2, Colibrick, and Net PAD use the same standard INT7 Connector.
Getting Started 2 Installation For easier modification of the wiring we supply the SV9 Terminal board (p/n SV9) with screw contacts for INT9, U-PAD2 or Colibrick A/D Converters. Connection of starting cables: Starting input reacts to a change of the TTL logical level ( 5V) or to a connection by any contact (button, contact of relay). Input implicitly reacts to a change from HIGH to LOW (or closing of a contact). The input function may be changed by switching the Down item of Ext.
2 Installation Clarity 2.5 Clarity Configuration Note: l l Clarity is automatically preconfigured for analogue acquisition with no control modules. However, even the users of analogue acquisition should review the following chapter to assign custom detector names and signal units. Start the Clarity station with the icon on the desktop. Invoke the System Configuration dialog using the System – Configuration… command. Fig 5: System Configuration dialog l Set the Number of Instruments field .
Getting Started 2 Installation Note: If necessary, add further equipment to the list on the left using the Add button in the lower left-hand section of the dialog. The configuration of particular control modules is described in the corresponding Clarity Controls manuals.
Getting Started 3 Qualification procedures 3 Qualification procedures The quality of analytical data is an important issue in many laboratories. One of the requirements for ensuring the reliability of generated results is the validation of all instrumentation and procedures that are used to acquire data. For chromatography data stations usually three levels of validation (qualification) are relevant: 3.
3 Qualification procedures Clarity Fig 8: IQ window l If the Installation Qualification fails, it is recommended to uninstall and then re-install Clarity. If it fails again contact DataApex support. Note: The most common reason for a "Failed" result is the installation of an upgrade over an existing full version of Clarity. This itself does not produce any errors but since some of the files are preserved from the original installation, the checksums will not match.
Getting Started 3 Qualification procedures The Validation kit (p/n: CVK ), as well as SST Extension (p/n: A22 ), can be purchased separately. The validation process is described in more detail in the Validation Kit manual (M039). 3.3 Performance Qualification - PQ The Performance Qualification (PQ) is a procedure confirming that the analytical system is fit for a given type of analysis. The overall system performance is tested against the requirements of the manufacturer specification.
Getting Started 4 Program structure and control 4 Program structure and control Clarity has a hierarchic structure. After start-up, the main Clarity window will be displayed with the symbols of the configured Instruments. After clicking on the chromatograph picture and entering the User Name (more information on User Names can be found in the Reference Guide) the Instrument window will be displayed. This window is used for acquisition and processing of data using the connected chromatograph.
4 Program structure and control Clarity All dialogs relevant for the performance of actions in the Instrument window can be easily accessed from the Instrument window by using the appropriate commands from the menu or by clicking on their icons. Note: In addition to the Clarity chromatography station, DataApex produces the Clarity Lite chromatography station. It is a less expensive, and simplified version of Clarity with limited functionality able to operate with only one Clarity Instrument.
Getting Started 5 Tour through the Clarity station 5 Tour through the Clarity station The following two sections will show you step by step,how to perform a single analysis (the chapter "Running the Single Analysis" on pg 17 .) and a sequence measurement (the chapter "Running the Sequence measurement" on pg 24.). They are shown as a succession of steps, all of which should be performed in the given order. Some sections may be skipped, as their output files have been included already as examples.
5 Tour through the Clarity station Clarity 5.1 Running the Single Analysis There is a simple project aimed on basic functions prepared for Instrument 2. It shows the way to start a Single Analysis, monitor the Data Acquisition and process the resulting Chromatogram. 5.1.1 Instrument window l l l Note: Start the Clarity station. The main window will appear, showing up to four configured Instruments.
Getting Started 5 Tour through the Clarity station 5.1.2 Single Analysis dialog Use the Single Analysis Single Analysis dialog. button in the Instrument window to open the Fig 11: Single Analysis dialog l l l l l Note: The fields in the Analysis section contain information about the sample. You may set the values in the fields as shown on the Fig 11 on pg 18 ., as typical analysis settings.
5 Tour through the Clarity station l l Clarity Run the analysis by clicking the Run button . The Single Analysis dialog will close now, but if you open it again, you will see three more buttons (Stop, Abort, Snapshot) , that will allow you to stop or abort the analysis or take snapshots (see the chapter "Data Acquisition window" on pg 20.). Close the Single Analysis dialog and return to the Instrument window.
Getting Started 5 Tour through the Clarity station 5.1.3 Data Acquisition window l l l In the Instrument window, look at the Status line (see Fig 10 on pg 17.). The acquisition is now signaled by the RUNNING state and the actual run time shown there. To see the data acquisition in process and possibly control it, use the Data Acquisition icon (see Fig 10 on pg 17.) to enter the Data Acquisition window. Depending on your station's configuration, one or more signals may be displayed.
5 Tour through the Clarity station l Clarity The Chromatogram window opens because the station is set to do so. These settings are available in the Instrument window: Fig 13: Post-run functions of the Instrument window l These icons can be in the position or , respectively enabling or disabling the opening of the given window or the printing of the report. Other postrun options including export of the data or running external program are available in the Setting - Postrun...
Getting Started 5 Tour through the Clarity station 5.1.4 Chromatogram window l The Chromatogram window can also be opened manually by clicking on l the Chromatogram icon in the Instrument window. The correct sample chromatogram might not open automatically in the Chromatogram window. To open it manually, use the File - Open l l Chromatogram... command or the open icon and select the WINE_ SAMPLE.PRM file and press the OK button.
5 Tour through the Clarity station l l l l Clarity corner of the graph (the active signal is set in bold), from the icons in the Overlay toolbar (the active signal has the debossed icon) or from the graph outline color and table headers color. The tables change by changing the active signal. Change the active signal by double clicking on its name in the legend section . Change the color of the currently active signal to another one by clicking on the Not used color icon in the Overlay toolbar.
Getting Started 5 Tour through the Clarity station 5.2 Running the Sequence measurement Sequence operation allows automated measurement of large numbers of samples for chromatographs equipped with autosamplers. Clarity provides the possibility to select an ACTIVE (start controlled by the station) or PASSIVE (start controlled by the autosampler) sequence. It is also possible to re-process already measured sequences.
5 Tour through the Clarity station l l l Note: Clarity calibration (or its recalibration, if there already were any data in the calibration). The Method Name column sets the template method used for measuring the sample. The Report Style column sets the print style used for reporting the measurement. Each row can have its own template method and report style; it is thus possible to measure according to several template methods in one sequence.
Getting Started (no chromatogram saved) or Stop be saved).
5 Tour through the Clarity station Clarity 5.2.2 Calibration window l Note: Use the Calibration Calibration window. button in the Instrument window to open the The following section describes how to make a calibration. If you wish to skip this step, you can open (via the File - Open Calibration command) the calibration file DEMO1.CAL instead and test the functions of the Calibration window on it. In this case you can continue with the chapter "Linking the calibration to a chromatogram" on pg 29.
Getting Started 5 Tour through the Clarity station Fig 17: Calibration window - loaded standard l l l l l l Set the calibration level number to 1 on the Current Level field . Use the Add All icon (blue) to move all identified peaks to the calibration table. The Calibration table appears in the Calibration window, ready to be completed as seen on Fig 17 on pg 28. As it can be seen in the calibration, individual peaks are now identified according to their retention times only.
5 Tour through the Clarity station l Clarity Set the third calibration level accordingly using the STD 3.PRM file and Amount of 3.0 and the fourth level (file STD 4.PRM, Amount 5.0) except for the ISTD peak (always Amount = 2 ). On the tabs of the individual compounds , the linear four-point calibration can be seen. Save the calibration file now using the Save Calibration CALIBDEMO.CAL into the default directory.
Getting Started 5 Tour through the Clarity station 5.2.4 Linking the calibration to the method In case of a large number of chromatograms, linking the calibration to each file separately would be a time-consuming process. To avoid this, the calibration may be linked to the resulting chromatograms automatically. l Return to the Instrument window and use the Calculation icon to open the Method Setup dialog directly on the Calculation tab .
5 Tour through the Clarity station Clarity Mark all files with the names SAMPLE_VIAL_X-Y in the DATA directory to be reprocessed, check the Reprocess by Instrument Method checkbox and click the Proceed button. All selected chromatograms will now have the calibration linked to it. Note: The chromatograms to be batch processed have to be saved in the current project directory. l Open the Chromatogram window and load any file just reprocessed (e.g. SAMPLE_VIAL_7-2.PRM) and look at the Result table.
Getting Started 6 Connecting Autosamplers 6 Connecting Autosamplers This chapter describes wiring of the autosamplers. The configuration varies depending on the type of chromatograph (GC or LC), sequence mode (ACTIVE or PASSIVE) and presence of optional control modules for direct control of chromatography equipment. Note: More detailed information on Clarity sequence modes can be found in the chapter "Sequence" in the Reference guide.
6 Connecting Autosamplers Clarity Variant A - started by closing the contacts The first diagram shows the wiring of an autosampler that will initiate the injection after its input contact is closed. Fig 19: Wiring of the autosampler - variant A The injection will start only after both serially connected contacts (Clarity and the GC) are closed. After an injection, the autosampler will close the INJECTION contact and thus the command to start the temperature gradient program will be given.
Getting Started 6 Connecting Autosamplers Variant B - started by opening the contacts In the second scheme there is autosampler wiring that conversely waits for output contacts to be opened. This requires different connection (marked by a circle). The OUTPUT and READY contacts are connected in parallel and the autosampler will start its operation after both contacts are opened.
6 Connecting Autosamplers Clarity 6.2 AS + LC set - Active Sequence In LC systems, the autosampler typically governs the timings. The eventual pump gradient or detector programs are set independently. Any autosampler that is used in the Clarity Active Sequence without an AS Control module must be synchronized with the Clarity station by cables.
Getting Started 6 Connecting Autosamplers 6.3 AS - Passive Sequence (GC or LC) The autosampler used in the Clarity Passive Sequence (both GC and LC sets) does not use the OUT n R digital output cable. All timings are controlled by the chromatograph; Clarity only performs one analysis for each start signal received. All synchronization only includes external start up of data acquisition in Clarity using the INn starting cable.
6 Connecting Autosamplers Clarity 6.4 Auto Sampler - Active Sequence + AS Control + A/D card When using the optional AS Control (p/n A26) module, all communication is performed through a separate data cable (usually a serial cable connected to a COM port). Caution: Refer to the corresponding Clarity Control manual for wiring specific to your control module. The following diagram shows a directly controlled autosampler with external digital acquisition by an A/D converter (INT9, U-PAD2 and Colibrick).
Getting Started 6 Connecting Autosamplers 6.5 AS - Active Sequence + AS Control + digital acquisition When using an optional AS Control module in combination with digital acquisition detectors (e.g. the Agilent 6890 module), the connection will be the following: Fig 24: Wiring of the autosampler with AS control module and digital acquisition Caution: Refer to the corresponding Clarity Control manual for wiring specific to your control module.
Getting Started 7 Troubleshooting 7 Troubleshooting If you will not find your answers here, use the www.dataapex.com www.dataapex.com website where the Support menu will navigate you to frequently asked questions (FAQ), Clarity forum or contact to DataApex helpdesk. Note: You may find other Error Messages and solutions for problems connected to particular hardware in its respective manuals.
7 Troubleshooting Clarity 7.1 Locate your problem: When troubles occur, the fastest way to find a solution for it is to search for it in the following index via the Dialog (window), in which the problem occurred, Error Messages that appear or according to the used Hardware. The name of the window/dialog is visible in its header. Note: Names of individual Clarity Instruments appear in the header instead of the common term “Instrument”. Tab 1: List of windows and dialogs Dialogs pg 41., pg 42., pg 43.
Getting Started 7 Troubleshooting 7.2 Problems at station start 7.2.1 DEMO - missing HW Keylock The Rockey (or Sentinel) protective key (dongle ) must be plugged in either a parallel or USB port and its driver must be properly installed. Several problems may cause this error message: ▌ Your protective key may not be installed properly.
7 Troubleshooting Clarity 7.2.2 DEMO - Keylock test failed ▌ There is a DEMO - Keylock test failed error message in the Clarity window. Fig 25: DEMO - Keylock test failed Description: Solution: Clarity has detected that the protective Hardware key was removed while Clarity was running. Re-install the Hardware Key and then go to the Help - User Code... command in the Clarity window and click on OK to force the station to update its status. 7.2.
Getting Started 7 Troubleshooting 7.2.5 DEMO (in the window header) ▌ The DEMO inscription is displayed in the header of the Clarity window. Fig 26: Clarity DEMO Description: Solution: If you only see the DEMO caption in the header of the main Clarity window without any further description, you have installed the Clarity DEMO version. Uninstall the DEMO version and install the full version of Clarity software. 7.2.
7 Troubleshooting Clarity 7.3 Problems upon collection of data 7.3.1 Data Acquisition - non-functional Gray icon with the heading "Disabled" and non-functional Monitor Data Acquisition command. Fig 28: Data Acquisition disabled Other manifestations of this error are also: Method Setup - Acquisition tab missing, Method - Acquisition command non-functional, Run , Stop, Abort commands non- functional in the windows Single Analysis and Sequence).
Getting Started 7 Troubleshooting ▌ c) The detector is not allocated to the Clarity Instrument: Fig 30: Detector not allocated to the Instrument Description: Solution: Note: Open the System Configuration dialog from the Clarity window using the System Configuration... command and check the tab of the corresponding Instrument Instrument X. If it has no allocated detectors, add them.
7 Troubleshooting Clarity 7.3.2 Data Acquisition - Simulated ▌ The title "Simulated" is displayed on the Data Acquisition window. Fig 32: Data Acquisition Simulated Description: Solution: The corresponding Instrument only displays the simulated curve (from the file CHANNX.DTA file), or in other words has allocated a DEMO detector to itself. Open the System Configuration dialog from the Clarity window using the System Configuration...
Getting Started 7 Troubleshooting 7.3.3 Other Error Messages You can find the description of other Error Messages and possible problems and solutions for them in other manuals. Here is the list of known possible Error Messages with reference to their descriptions: Tab 4: Other Error Messages Error Message Board Malfunction Cannot create detector Cannot find driver file \\.\CSWINT70 Cannot find driver file \\.
7 Troubleshooting Clarity 7.4 Hardware Key 7.4.1 Rockey USB dongle (re)installation Fig 33: Rockey USB dongle l Install Clarity software. Caution: l l l l l l l Be sure to have suitable drivers at hand before inserting the USB token into the PC slot for the first time! Connect the USB dongle to a USB port on the computer. Use the INSTDRV.EXE file from C:\CLARITY\HW_ DRIVERS\ROCKEY\ folder to (re)install the Rockey drivers.
Getting Started 7 Troubleshooting 7.4.2 Rockey LPT dongle (re)installation Fig 34: Rockey LPT dongle If you encounter problems with printer port Rockey hardware key, then: l l l l l l l l Verify that the key is properly inserted in the printer port. Navigate to C:\CLARITY\HW_ DRIVERS\ROCKEY\ directory in the file manager (e.g. Windows Explorer). Run the INSTDRV.EXE file to invoke the Setup Wizard. Select Repair option in the first dialog and click Next.
7 Troubleshooting Clarity 7.4.3 Sentinel dongle installation Until Clarity version 2.4.1 the dongle had to be installed and present in the PC only when using either the Clarity Offline version or when using digital acquisition (e.g. via control module) without an A/D converter. Later versions always require the dongle. Printer port dongle Fig 35: Printer port dongle The drivers are automatically installed during the installation of Clarity station.
Getting Started 7 Troubleshooting 7.5 System Files (systeminfo.txt file) The C:\CLARITY\SYSTEMINFO.TXT file contains valuable diagnostic information. Its contents can also be displayed in the Clarity Help – About – System Files dialog. Fig 37: Help - About - System Files The file contains the following information (these are examples of what the listings could look like. The information in the program section is visible in the Help - About - System Files dialog.
7 Troubleshooting Clarity station, number of Instruments allowed, extensions available, purchased control modules, type and serial number of the hardware key and list of A/D converters/detectors connected to the computer and configured in the station. The registered files entries should match the installed files in version and location. If there were any discrepancies, this may cause some problems. 7.
