For ESTD calculation, the Amount (%) column will give you the normalized % (i.e. % based on sum of individual peak amounts), as long as the Sample amount field is 0 (default value). All peaks in chromatogram should be identified and calibrated.

This problem is caused by HP ProtectTools suite, installed on most new Hewlett-Packard computers. The particular file responsible for this behavior is DPAgent.exe, purposed for controlling the fingerprint scanner.
The easiest solution of the problem is to rename this file, thus it will be not automatically launched after startup of the computer. Standard location of the file is C:Program Files (x86)Hewlett-PackardHP ProtectTools Security ManagerBinDPAgent.exe, however it may differ slightly on different versions of the suite. For fixing the problem, the file has to be renamed (we recommend to rename it to DPAgent.bak.exe, thus it can be easily renamed back when necessary).
In case you need to use the fingerprint scanner, it is also possible to terminate this file only when you intend to launch Clarity datastation. It can be made manually (using Task Manager) or facilitated by some utility able to kill a process running on the computer.

This file collides with other programs too: http://www.file.net/process/dpagent.exe.html

ou can open the chromatogram on the Clarity Instrument which is in Offline mode. In Clarity - System Configuration, increase the Number of Instruments option in the top right part of the window. Even if you have license for one Clarity Instrument, you can use other Clarity Instruments without measuring data from detectors or controlling your instruments. This can be helpful for evaluating chromatograms without turning on the instruments in your lab or if you use the Clarity, for example, in your home - see FAQ bout running Clarity on on multiple computers using 1 dongle (hw key).

Yes, it is. Simply take your hardware key (dongle) and plug it in another PC. You can install Clarity on as many PC as you like using the same user code. The Clarity will work properly on the one PC with the hardware key connected. In such a situation, FAQ Evaluating a chromatogram without starting the communication with instruments may be handful for you.

Precondition:

The Retention indexes columns are hidden in the default layout of Clarity tables.
To display them in both the Calibration window and the Chromatogram window:

1. Open the Calibration (Chromatogram) window.
2. Point cursor in the calibration table (or Results table in chromatogram) and click the right mouse button.
3. A local menu will pop up, select the Setup Columns command.
4. In the Setup Columns dialog select Reten. index in the hidden columns list and click Display button and then OK.
5. Now the Retention indexes will be visible in the table.

To set the indexes:

1. In the calibration table, fill the Retention indexes to the corresponding peaks. The other peaks leave at zero value
2. Do not forget to save the calibration.
3. Open the chromatogram, that uses the calibration.
4. In the result table you will see the retention indexes.

See the screenshots:

Unretained peak:

If you need to use the Unretained Peak, follow these steps:

1. In the Calibration window, open the Calibration Options and turn on the Retention Indexes with Unretained Peak option.
2. You can change the Unretained Peak [min.] value in the Method Setup - Advanced tab.
3. If you want to change the value in the Chromatogram, click the Results - Performance Table menu in the Chromatogram window first.

At first check, if the U-PAD2 isn't connected to a USB hub. Problems are mostly related to the USB power supply, so definitely the hub should have external power source.

Note the U-PAD2 is sensitive to communication delays. Responsible for those delays on USB communication may be the computer hardware or software. Processor overload, low RAM memory or running processes blocking the processor or communication lines should be checked. In case the communication is interrupted for more then 10 seconds, an error will be invoked. Error message "No data from Acquisition", "No data received for ..." and similar may appear randomly. As a consequence, the running acquisition is stopped and the running sequence interrupted. In case the problem is temporary, sending of the method again may solve the problem.

Try the Task Manager and inspect the processor load and processes consuming large amount of CPU time or memory. Suspected programs are incorrectly set anti-virus (continuously checking file types used by Clarity during data acquisition. The *.raw, *.prm, *.audit, *.tmp file types should be avoided diabled for scans. Any other programs monitoring files on exchangeable media (i.e. programs for organizing and presenting of pictures, music or video, including some CD/DVD burning programs) may also interrupt the Acquisition.

Also, when the Acquisition is running, it may be interrupted by any actions started during this, like a printing to a slow USB or network printer, large file transfer over network or USB, connecting or disconnecting USB devices, computer entering sleep mode or screen-saver activation.

This problem is caused by the wrong configuration file saved when the computer was shut down while Clarity was running. Normally, Clarity saves data to its configuration file when exiting. When the computer is shut down while doing this, the clarity.cfg file may be corrupted and cannot be used in Clarity next time it is opened.

The corruption of the clarity.cfg file may happen in numerous ways - when the computer is switched of while the Clarity is running, while experiencing some fluctuations in the power system or, which seems to be the cause of your client according to the lunch time, when the computer is switched to the sleep mode while Clarity is open, but not running. While the analysis in Clarity is running, Clarity can block the switching to the Sleep mode, but without an active analysis, it can't do so. Thus, when in sleep mode, the computer loses the communication between Clarity and the A/D converter and/or hardware key, and Clarity switches to the Demo mode, destroying the configuration. Backup configuration must be used than.

To solve the problem: All data, such as methods, sequences, data files, calibrations etc. are saved on demand, and are not corrupted when simmilar situation arises. On the other hand, the clarity.cfg file holds the information on the path to these working directories (if set in the Directories dialog accessible via the System - Directories command from the main Clarity window). It is thus necessary to set these directories or select the project that was used before once more on each Clarity Instrument. Unfortunately, the clarity.cfg file is corrupted and the System Configuration settings are lost, so they must be set in the System Configuration dialog manually once more. To repair the damage, follow this process:

• Open Clarity and ensure that you are not in the DEMO mode (there would be Clarity DEMO written in the heading of the main Clarity window). If you are in the Demo, use the Help - User Code command to enter the correct User code.
• Open the System Configuration dialog and configure your system manually (eg. add detectors, LC's, GC's, valves and so on to the configuration, fill in their settings as desired, and distribute them to particular instrument, as intended.
• Close the System Configuration dialog and exit the station. The clarity.cfg file was now saved with the correct settings of the configuration.
• Open the Clarity once more.
• If you had the Directories dialog set before, use the System - Directories command from the Clarity window to set it once more. Then, close the dialog.
• Open the Instrument. You might get the information simmilar to "the current method was prepared on different configuration. Some parametres will be used in default format", if you opened and then saved the method after the clarity.cfg file was corrupted.
• Load the desired project to the Instrument; Default clarity.cfg file has Work1 directory set as the project directory, you have, most probably, created your own project before the shutdown. Use the File - Project command, select the appropriate project from the list and press the Open button.

The station should now be in the configuration as before the fall. If the method was opened and saved after the fall of the configuration, there might be necessary to check/set some parametres, mainly on the Method Setup - Acquisition and Method Setup - Measurement tabs (as the demo mode resets the settings of detectors and removes them from the configuration).
To prevent from happening this in future: supposing that the cause of the problem was really the sleep mode of the operation system, switch it off according to the following procedure:

• In windows XP, use the Start menu and open the Control Pannels. There select the Power Options icon (you may have to switch to the Classic view).
• Set the System standby and System hibernates options to Never (as shown in the picture).

• Apply changes and use OK to exit this dialog.

The corruption should be prevented for the future. Of course, if it was caused by another reason, such as instabilities in the power network, only good stabilized backup power source may help.

If you add a User Column both to the Summary and Result Table containing the same formula, often you cannot get the same results. In Summary Table you cannot use the First, Last, etc. functions from Special Values. For example "[Reten. Time]first/[Reten. Time]" will not work here. But you can use figures working with the compound itself, for example "[End Time]-[Start Time]".

In case of calibrated groups the columns Amount and Amount [%] sums all calibrated groups plus all  peaks which are not part of any group.

Prepare a batch file (clarity.bat) to perform the required tasks using the command line parameters:

The batch should contain the following line (example):
start C:Clarity_Demo_304Clarity.exe i=2 u="Administrator" psw="" seq=C:Clarity_Demo_304FCFC3.seq run_seq=2

Explanations:

• start C:Clarity.exe will start the Clarity in specified directory
• i=2 will open the desired instrument (2)
• u="Administrator" psw="" will open it as a specified user with specified password (essential, otherwise it stay waiting for this input)
• seq=C:Clarity_Demo_304FCFC3.seq specifies the sequence to run
• run_seq=2 starts the sequence on instrument 2

Prepare the sequence to be started.

The sequence can contain just one line with the Start up method, or some standards/samples can be defined in the following rows. In the start up method, define to switch the lamp on and flush the system as required to equilibrate.

Use the Task Scheduler

Set the clarity.bat to be started at defined time and date The Scheduler is located in Windows Start menu, Programs, Acessories, System Tools, Scheduled Tasks. Use the advanced properties of the task to fine tune the scheduling

Set the task to be started when you are logged on only and when leaving the PC, do not log yourself off. Remember, there must not run Windows Update which may log you out and restart the PC.

When in Overlay mode one of Move, Scale or 3D View commands is used, all the information about retention times, height and area of peaks are not displayed (as there will be mismatch between result table and the displayed chromatogram). Chromatogram modified by this types of commands could be saved using the Chromatogram - Overlay - Mathematics - Copy command and evaluated or the axes Offset and Scale need to be restored to original values.

FFT filter is suitable for signals with a high noise and small peaks.

Warning: For a chromatograms with high signal/noise ratio (over 500) visible artefacts can be created at the base of narrow peaks.

Normally, the Active Sequence sends a command to the sampler (over serial line or by digital output) and waits for the start signal from the detector (again over the communication line or digital input). The digital input and output used for this are specified in the Clarity Configuration - Ext. Start Dig. Input (digital input) and Ready Dig. Output (digital output).

In case the injection is performed by some controlled valve or instrument (typically EAS analyzers) not supporting the Injection marker by digital output, the common solution when using DataApex A/D board is to interconnect the digital output set for Ready Out signal directly to the digital input set for Start In command. The digital input on the instrument starting the next run will be connected in parallel. With controlled valve, the injection is then performed during the actual run by switching the valve (or valves) from Clarity Event Table.

In case no A/D board is used and the devices are not offering those digital inputs and outputs (for example with Agilent GC 5890), the suggested workaround will be to use the DataApex Virtual Digital Input Output Loop (auxiliary device, requires A24 LC or A23 GC Control license) to simulate the input/output needed - (those are virtually interconnected).

Yes, but the sequence allows the chromatograms to be stored only in the subdirectories of current project directory. The subdirectories need to be created using an external file manager (e.g. Windows Explorer) before it can be used in Clarity. The path will be specified in the File Name column as a relative path only, i.e for C:\Clarity\Work1\Data\MyProject\ChromatogramName you have to set the filename as MyPyproject\ChromatogramName.

This limitation is necessary to allow the opening chromatograms from sequence and to perform complete reprocess of the sequence from the Batch dialog accessible using the Analysis - Batch command from the Instrument window.

Cannot find driver file

• When Clarity cannot find the device's kernel driver (*.sys file). Try to reinstall the drivers. Follow instructions in the Troubleshooting section how to reinstall the device of the respective hardware's manual.
• When  the device is configured in Clarity but it cannot be found it is inserted to the mainboard's PCI port. Check, whether the card is correctly inserted. Also the card can be nonfunctional.

Cannot load device driver

• Probably the card (Int7, Int9, ...) isn't located in the PC or is incorrectly inserted into the PCI port.

Cannot find first board

• One of the A/D cards (Int7, Int9, ...) A/D converters didn't pass the test. The card is probably broken.

Cannot find second board

• You tried to add to Clarity Configuration second Int7/Int9 board, but in your PC is located only one card. If you have two cards, check, whether are both of the correctly inserted into the PCI port.

Board malfunction

• The A/D card in the PC is inserted correctly, but it didn't pass the test of the device's A/D converters chips. Probably the card is broken or the PC is overloaded by other programs activity.

Incompatible device driver

• Very rare situation, when there is incompatibility in the device's kernel driver (.sys file) and the Clarity module (.dll file). Follow instructions in the Troubleshooting section how to reinstall the device of the respective hardware's manual.

UPAD device malfunction, NetPAD Device Malfunction

• When connected to the PC, the U-PAD or U-PAD2 didn't pass the test of it's A/D converters. Probably the card is broken or the PC is overloaded by other programs activity.

For LAN communication, one of the 1100/1200 modules must be equipped with a LAN communication card inserted in the MIO slot on the back side of the module (do not mistake it for the CAN connectors used for the internal system communication, using the same RJ45 connectors).

Original board supported by Agilent is a G1369A LAN Interface described in Agilent G1369A LAN Interface User Manual (Agilent P/N G1369-90000).

Alternatively you can use J4100A JetDirect card - reportedly this board is functionally identical to the HP JetDirect Print Servers 600N/400N/500X/300X.

Warning: Please, test it before buy, those cards may cause problems and the communication may be unfunctional.

To purchase, you can use:

http://www.chiralizer.com/usedequip.htm HP/Agilent MIO / LAN Interface Card

Item #J400N-1: An as-new, fully tested HP ChemStation Rev A or B Ethernet interface Card. This cards slides into the back of most HP/Agilent HPLC's (1100 and 1200-Series), UV/VIS (8453) and 35900E A/D boxes to provide LAN Ethernet (RJ-45) communication to your computer. Includes the most recent firmware version, K.08.49 too. *Can also be used as a Print Server Card for some LaserJet Printers. Agilent charges ~ $800 for a new one. Our Price : $ 200.

Yes, Clarity supports SimDis Expert® 9 from Separation Systems. Clarity can be configured to automatically open and process measured chromatograms in SimDis Expert.

For more details, see the datasheet Using SIMDIS Expert® 9 (Separation Systems) with Clarity .

Yes, from Clarity ver. 3.0 you can add a User Column which display RRT according to a Compound Name. To do this, follow the instructions:

• In the Chromatogram, you need a defined peak name from Calibration Table which will be used for calculation of other peaks RRT. Alternatively you can name a peak directly in the chromatogram by using the Force Peak Name function.
• In the Result Table of the Chromatogram window, add new User Column and in the Expression field, add [Reten. Time]/[COMPOUNDNAME$Reten. Time], where COMPOUNDNAME is the Compound which will be used as reference peak to calculate the retention times. You can generate the calculation by choosing the Reten. Time in the Columns field, then the "/" sign, and for last, click the Special Values button and click on the Comnpound item. Type name of the column in the Title field and hit OK. New column appear in the Result Table containing the calculated RRT. See the image below.

Yes, it is possible. The function that does so is the same as for adding a new peak - Add Positive. Select the Add Positive function, choose the part of the unresolved peak which you want to split off and add the interval markers to the borders of the new peak. Both peaks will be separated by a vertical line now. Including the current peak's maximum in the interval would produce no result.

PDF Reports in Chinese requires two prerequisities:

• You have to install True Type font supporting Chinese signs on your system.
• You have to set this font to use in Clarity reports: Set it in Clarity - Instrument - Report Setup dialog - Page Setup tab.

Then the reports will be printed properly. There is no need to install the font on other computers, where the PDF Reports will be for viewed only.

This mostly happens on black and white printers which falsely informs Windows that they are color printers. In Report Setup Instrument window - Page Setup tab, check the Black and White Print option. Then all the printed text should be visible.

In case the computer is connected to the Internet, just select the menu Help - Check for Updates in the Clarity main window. New version will be offered. You may need to fill in the registration form and proceed with selecting the default options suggested. Please note, a window requiring computer restart may pop up during the installation, select no and proceed with installation until finished.

Alternatively you could download the version from our web pages, section downloads - full versions. Again, you need to login or fill in the registration form.

Most chromatography systems use a proprietary data format (the main reason is belief that it ensures data integrity for GLP-related requirements). To open and process such chromatograms in Clarity, they must be first exported from the original software in a suitable format. Most commonly used is the AIA (.cdf files) or ASCII (.csv, *.txt, *.asc and other files) formats.

Clarity can import such a files (only the chromatogram data, not integration method or result tables) and process them using the current instrument method.

Chemstation

• The export is available with full menus active in Data Analysis view, menu File, command Export file, AIA file....). Due to the way the Chemstation exports the files (they are always named signal01.cdf and stored in user named folders, batch export is not supported), processing is not very convenient and will be quite laborious for a large number of files.
• The export of DAD data is even more complicated if not impossible (you will have to export each wavelength separately and combine them to the format which can be imported to Clarity).

EZ Chrom

• The chromatograms can be exported during processing, in the Advanced Method Options, Export tab for option Chromatogram the AIA and ASCII formats can be selected.
• The ASCII  *.asc file format is supported by Clarity both for chromatograms and 3D data. AIA files can be used as well.

These problems may occur during the Setup of an Hardware (Int7, Int9, U-PAD2, ...) in the Clarity Configuration.

Error on setup

Problems on a low level, either a kernel driver or hardware itself.

Can't create ... (device name)

Usually a problem with the control module library.

The *.dll file is either:

• not registered,
• not compatible with the current cswext.dll,
• registered in a different directory and thus using a different cswext.dllversion than the Clarity.exe.

Solution

Uninstall the previous version and then install Clarity again. This usually helps. Follow the chapter for reinstallation in the device's manual.
Alternatively it is possible to register the corresponding *.dll file using the Windowssystem32resvr3.exe program.

Yes, Clarity can be connected to any LIMS using the import/export of text files. Results can be exported in various formats to the LIMS and the sample info can be imported from a TXT file into Clarity Sequence which you intend to process.

There is a dedicated program interface LimsLink which can be used as an intermediate, however most LIMS systems will be able to handle the import/export of the text data directly. Please, see our white paper describing the Clarity cooperation with LIMS: clarity-lims.pdf.

Yes, Calibration Bracketing is supported directly in Clarity since version 3.0.

What is bracketing?

The bracketing in calibration is a technique, when samples in a long  sequence run are evaluated to standards immediately preceding and  immediately following the respective samples. It is used to compensate  for instability of detector response during the run, for example typical  for electrochemical detectors.

Bracketing in Clarity 3.0 and later

1. In the Method Setup - Calculation, set the name for cloned calibration files used during the Calibration Bracketing.

The field enables the use of any text, however it is recommended to  use  variables appropriate to the calibration method (Line, Date and  Time, ...).

2. In the Sequence - Sequence Options, check the Calibration Bracketing option.

This sets the sequence and calibration to the Calibration Bracketing   mode. As every unknown sample series is demarcated by calibration  standards  and as such uses a single calibration file, calibration will  be cloned from the  previous calibration clone whenever an unknown  sample or blank follows the  calibration standard. In a newly cloned  calibration file, all responses other  than responses of the last series  of calibration standards (only those standards  that follow the unknown  samples) are cleared.

This may cause incorrectly set Peak Width parameter.

Clarity Peak Width (PW) parameter affects two things:

• Peak detection algorithm i.e. what will be considered as a peak, peak start and peak end position.
• Sample bunching, i.e. how many samples will be summarized as one data point. It can be imagined as a very simple signal filter which makes the signal smoother. The formula is that approximately 30 data points is necessary for peak detection. So for instance if you set PW=1min and Sampling rate is 100 Hz, each series of 200 points will be displayed as one point (60*100/30).

In case you can't find a toolbar button or command you can see, for example, in documentation, click the View - Reset All menu item. All buttons will be reset to their default positions. You can find this function in most Clarity windows where the toolbar buttons are located.

Rarely, if you can't locate the main menu, press Alt-V to display the hidden menu.

For Int7 and Int9 cards, the full height PCI slot is required, otherwise the card cannot be used with your PC. Mostly the problem occurs when you have some mini version of PC or slim case, etc.

Also, ensure you are trying to insert the card into PCI slot, not to PCI Express. Int7 and Int9 cannot work with the PCI Express slots.

For preparative purposes a multiposition valve are frequently used as a simple fraction collector.

Knauer provides dedicated control modules for multiposition valve based fraction collectors, however they are available solely in the ClarityChrom Prep OEM version.

To use valves for this purpose in Clarity, it is necessary usually to combine a two position (three way) valve to perform the Collect/Waste function and a multiposition valve to perform the Next vial function.

Clarity Valve control modules also support the needed Next position command. Using the General Purpose Fraction Collector module (requires A24 LC control module)  and one of the controlled selection valves (Upchurch, Vici-Valco or Rheodyne MX II series), the fraction collector can be easily created.

In case a signal in Data Acquisition window and chromatograms is cut below 0 Volts, you probably unchecked the Bipolar option in the Setup dialog of DataApex's converter (Int9, U-PAD, ...). to fix this, open the Setup dialog of respective converter in the Clarity Configuration and check the Bipolar option again and both positive and negative voltages will be measured.

Because the File Created info in the Windows Explorer or any other file manager program informs when the file was created in the File System and this can be different from data of acquisition (when the chromatogram was saved as new one, rewritten, etc.).

You can find the real acquisition date of chromatogram in:

• Chromatogram window - Measurement Conditions tab - Instrument subtab - Sample Identification box.
• Archive/ Restore window - Date column in the File List.
• Acquired label in the Print Report.

In this situation, it may be incorrectly set-up the e-mail client (Outlook, Thunderbird, Eudora, The Bat!, ...) in Windows.

1. Ensure you have installed your favorite e-mail program.

2. Open Control Panel - Internet Options dialog - Programs tab.

Windows XP

3. In the E-mail field choose your e-mail program from the drop-down list.

Windows 7

4. Click the Set Programs button, then click Set your default programs link, select your e-mail client in the list and then click the Set this program as default button.

5. Try to send the report again, Clarity should now open new email window with attachments required for the report.

When the Send chromatogram by e-mail, Send Method by email or Send Calibration by email does not work, but th Send Report by email works fine - mostly the problem is in Microsoft Outlook Express, which cannot add locked files as attachment (they are currently open in Clarity). Try to use another Email program (MS Outlook, Thunderbird, The Bat!, Eudora, ...), this error was not found in Outlook Express at this time.

If you encounter the problem also with the Send Report by Email function, look at another FAQ describing this problem .

Problem

The USB or LPT Hardware Key is not properly installed.

Symptoms

• The "DEMO - missing HW keylock" inscription in the Clarity main window

Solution

Before you will do anything, ensure the corresponding port (USB, LPT) is enabled in the BIOS settings (integrated peripherals). The drivers can be install even if it is not enabled, however the key will not function then.

Depending on type of Hardware Key you get with the Clarity, continue with the proper chapter. See images below:

Rockey USB	Rockey LPT	Sentinel USB	Sentinel LPT

Rockey USB

• Remove the key from the computer.
• Use the instdrv.exe from the installation CD, HW_DriversRockey (alternatively you can download it from http://public.dataapex.com/rockey.zip ).
• Run the installer with the option Remove.
• It is not necessary to restart the computer when requested.
• Run the installer again with default settings.
• When finished, insert the key

If it will not help, please check, if the used USB port is functional or try to install the station on another computer.

Rockey LPT

1. Verify that the key is properly inserted in the LPT (printer) port.
2. In filemanager (e.g. Windows Explorer) navigate to C:CLARITYHW_DRIVERSROCKEY
3. Run the "InstDrv.exe" file to invoke Setup Wizard.
4. Select Repair in the first dialog and click Next.
5. In the second dialog check the Install parallel driver checkbox.
6. Select the Detect the parallel business radiobutton and click the Next button.
7. In the third dialog click the Complete button.
8. You will be asked to Restart Windows.
If this will not help, then contact our technical support.

Further observed limitations of the LPT hardware key

• Rockey LPT key does not function on LPT2 and higher, it can be used only with LPT1
• Rockey will function only on onboard LPT ports and ignore the ports on PCI cards.

Sentinel USB

• Remove the key from the computer.
• Use the Sentinel Protection Installer from the installation CD, HW_DriversSentinel.
  (alternatively you can download it from http://public.dataapex.com/sentinel.zip .
• Run the installer with the option Remove. It is not necessary to restart the computer when requested.
• Run the installer again with option Custom installation.
• Disable the installation of Sentinel Protection Server and Sentinel Keys Server. See the image below:

• When finished, insert the key.

If it will not help, please check, if the used USB port is functional.

Sentinel LPT

• Use the Sentinel Protection Installer from the installation CD, HW_DriversSentinel.
  (alternatively you can download it from http://public.dataapex.com/sentinel.zip .
• Run the installer with the option Remove. It is not necessary to restart the computer when requested.
• Run the installer again with option Custom installation.
• Disable the installation of Sentinel Protection Server and Sentinel Keys Server and enable the Parallel Driver. See the image below:

General Clarity Limitations

• Installation to program files: In Windows Vista or 7, the folder Program files is protected, however Clarity needs user access to the data and system files. It is not recommended to install Clarity there.
• Clarity must be at least version 3.0 or later.

DataApex Hardware

• U-PAD1 and CB20 board are not supported on 64 bit systems.
• INT9 does not work properly on some computers after waking PC up from sleep. It seems to work (no error message) but it gives no data. Solution - to disable and then enable INT9 in the Device Manager.

Control Modules and Tools

User Account Control (UAC) needs to be disabled during installation of some control modules (CTC PAL, Shimadzu LC systems)

To install the CTC PAL autosampler or Shimadzu LC-10/20 system it is necessary to disable the UAC (User Account Control) during installation, otherwise it will be unsuccessful. Similar problems were reported for installation of the Agilent 1100 system, again the UAC disabling helped.

Gilson pump control

Currently the GSIOC driver compatible with Windows Vista is not available, the control of Gilson pumps is thus not possible in this operating system.

Merck-Hitachi LaChrom Elite

Problems with detecting the.LaChrom Elite system were observed on Windows Vista and Windows 7 - attributed to the Hitachi driver

Registration of files in Windows Vista or 7

If you manually copy a control module DLL (i.e. not using an installer) you have to run the regsvr32.exe with administrator rights (select Program files, Accessories, Command prompt, right click to open menu, select Run as administrator and type the respective command line, i.e. regsvr32.exe and path to the dll), otherwise error message with code 0x8002801c will appear.

See also Table of compatible Windows OS, Clarity SW and our Hardware

• http://www.dataapex.com/product.php?id=clarity-std-compatibility.php.

Mostly you need appropriate new User Code only. Hardware key (dongle) keeps basic serial number XX-YYYY only and all information about valid version, number of instruments, extensions and control modules are part of User Code.

Only when upgrading from Clarity Offline to Clarity or Clarity Lite it is neccesary to replace the hardware key by new one.

No, it is not possible. If you try to open another version of curently opened chromatogram even Overlay mode is On the current version will be replaced by required new one.

The window is divided by movable splitters, most probably you have moved accidentally the splitter to the window border. Try the command Show both from the View menu.

In case of a wrong driver installed, the manual re-installation may help in some cases. This situation may occur for example when the Int7 or Int9 board is inserted into PC before the Clarity and drivers are installed.

Solution

Refer to manuals of respective board Int7 or Int9, locate section Troubleshooting and chapter Manual Installation. Follow instructions regarding to your operating system.

The system files store the following informations:

• C:ClarityClarity.cfg
  This file stores besides the hardware configuration information also information about the last user logged to a specific instrument and the custom instrument pictures used in the Main window.
• C:Clarity*.dsk
  These files store the information about the last used project *.prj and the individual user preferences (windows configurations and layout, tables and graph preferences, user columns etc.). The Clarity.dsk file from the PGM subfolder on the installation CD is copied during installation and used as a template for the *.dsk files of newly created users.
• C:ClarityProjects*.prj
  This file stores the info about the project subdirectories (the project directory has the same name as the project *.prj file) and the last used method, sequence, SST method and chromatograms.
• C:ClarityProjectsClarity.psw
  In this file the list of users and access rights are saved.
• C:ClarityProjectsClarity.sno
  This file contains the User Code.

The information about report setup, window layout, user columns and some other parameters for individual windows and instruments is stored for each user in the respective *.dsk file. Those parameters are not linked to specific methods or projects.
Custom instrument picture are placed in the Images subfolder on the installation CD. The new sequence and calibration files are created for the respective template files stored in the Common folder, only when not found there, the program defaults will be usedDefault Report styles are stored in the Common folder, each windows remembers the last used report style, this info is stored in the user *.dsk file.

Error message "No data from Acquisition", "No data received for ..." and similar may appear randomly. They are usually caused by some delays on the communication line - the data are not received in expected time and this causes the error message. As a consequence, the running acquisition is stopped and the running sequence interrupted. In case the problem is temporary, sending of the method again may solve the problem.

The underlying cause is usually the computer hardware or software responsible in the communication delays. Processor overload, low RAM memory or running proceses blocking the processor or communication lines  should be checked.

Triggering actions may be a printing to a slow USB or network printer, large file transfer ower network or USB,  connecting or disconnecting USB devices, computer entering sleep mode or screensaver activation.

Suspected programs are incorrectly set antivirus (continuous checking of file types used by Clarity during data acquisition - raw, prm, audit, tmp should be avoided), programs monitoring files on exchangeable media (i.e. programs for organizing and presenting of pictures, music or video, including some CD/DVD burning programs).

Analog input cables for Dataapex A/D cards

Recommended maximum lenght is 10 m.

Up to 30 m were used in some cases, however some signal loss or interferences could not be exluded.

RS-232 serial communication cables

The maximum cable lenght depends mainly on the cable quality and a baud rate used. Fairly long cables can be used for baud rates 9600 or less, for 19200 baud a maximum of 15 m is recomended and the lenght will decrease rapidly with a baud rate used.

For more details on serial communication see:

http://en.wikibooks.org/wiki/Serial_Programming:RS-232_Connections

USB cables

It is recommended not to exceed the 3 m cable length.

LAN cables

The lenght will depend on the cable quality, whether you user switch, etc.

Yes, using the Snapshot button accessible from Data Acquisition, Analysis or Sequence windows. Remember, the snapshot chromatogram will rewritten by the one from the finished analysis.

Command Export Data exports  Result or Summary Tables, chosen Method Parameters and Chromatogram's header  eventually Chromatogram data into various file formats, including MS Excel. What parameters to export you can select in the Export Data dialog. Use this function if you want to process the measured data/parameters from the chromatogram in database, spreadsheet or LIMS application.

Command Export Chromatogram exports the measured chromatogram in TXT or AIA format. Use this function, if you want to open and process the chromatogram itself in another Chromatography Datastation application.

If you use Clarity 2.7 and later, use Launch Manager - utility which is a part of the installation. See Clarity Help for more information. If you use an older version of Clarity, the best option is to upgrade to the latest version.

Optionally you can start Clarity using different shortcuts with specific command line parameters for each configuration. Each configuration is stored in separate *.cfg file and Clarity command line parameter sets the name of the corresponding configuration file. See Clarity Help. But remember, this is what the Launch Manager do including other useful features.

The recommended procedure for H53 method integration in Clarity:

1. use the same Peak Width and Threshold as in standard integration. Do not attempt to increase the Peak Width - this parameter causes a bunching of data as a side effect.
2. apply Baseline - Together to the whole chromatogram
3. apply Baseline - Forward Horizontal to the whole chromatogram
4. mark all the peaks between C10 and C40 as a group
   (the group boundary lines may exceed into the C10 and C40 peaks, only fully contained peaks will be included)
5. amend the peak starts and ends by manual peak tools if necessary for the C10 and C40
   (use the Peak - Both, with the A time corresponding to the respective C10 or C40 time and B time positive or negative respectively. The times are relative, i.e. will be shifted accordingly in other chromatograms).
6. create calibration file for C10, C40 and Group A peaks.

To subtract a baseline, in the Method Setup - Advanced dialog, set the baseline chromatogram and in the Matching set No Change. The baseline file should be acquired on stabilized system and preferably without injection of solvent or at least with lower volume of the solvent - otherwise negative artifacts will appear, which will interfere with the correct baseline setting in Clarity.

There is a condition that must be met:

When the chromatogram is integrated appropriately, use the Method - Save as Template command from the Chromatogram window to save the method as a template method, thus it can be opened on Instrument and used for further measurements.

Example of evaluated chromatogram

Sample data for Clarity

• DIN-H53.zip - zipped chromatograms method and calibration.
• Din-H53-processed.zip - zipped Clarity Project to load from Clarity. Unzip it and use Archive/Restore function in Clarity.

There are a couple of differences between analogue and digital acquisition:

• In analogue way there is the following chain in modern detectors: analogue detector unit, detector A/D converter, detector processing unit, detector D/A converter, analogue cable, Clarity A/D converter (U-PAD2, INT9, etc.).
• The digital chain is much simpler: analogue detector unit, detector A/D converter, detector processing unit, digital cable (USB, RS232, etc.), Clarity Control Module.

You can see at least three source of problem in analogue way:

• Detector D/A converter.
• Analogue cable.
• Clarity A/D converter (U-PAD2, INT9, etc.).

So there might be a significant difference between analogue and digital signal quality. It depends on many factors like:

• Quality of detector D/A converter (analog output resolution may be worse than digital).
• Length and quality of analogue cable.
• Proper cable connection (symmetrical, non-symmetrical).
• Absolute level of analogue signal (lower signal is more influenced by interferences from other laboratory devices).
• Proper A/D converted voltage range set (most typical problem is that a detector maximum signal is 10-100 mV only and U-PAD2 voltage range is set to 10 V. This leads to decrease of the voltage step resolution by 100-1000x!
• Proper sample rate frequency set at all three converters, see FAQ How to set proper Sampling Rate?.
• Proper peak width parameter, see FAQ How to set proper Peak Width parameter?.

The Sample Rate need to be set to provide enough points to adequately describe the  peaks of interest. Recomended is at least 30 points per the narrowest peak width. The default 10 Hz (for DataApex A/D boards) is suitable for most HPLC and packed column GC applications, the capillary GC and CE applications may need higher sample rates.

Acordingly to Sampling Rate, the Global Peak Width parameter has to be also amended. See also FAQ How to set proper Peak Width parameter?.

There are two instruments = 2 time basis. The configuration is as follows:
Clarity software for 1 instrument p/n C50
Single instrument Add on p/n C55
Dual channel A/D converter (external U-PAD p/n U2 or internal INT7 p/n I72).
See the Clarity configuration examples to learn more about the configuration options.

Yes, the total number of channels per one Instrument in Clarity is 12. In addition, if you have multiple A/D cards and U-PADs connected to PC, their channels can be combined variously on Clarity Instruments. The only limitation of maximum A/D cards and U-PADs depends on your PC's performance. See also examples of Clarity configurations.

When running Clarity on very slow PC or laptop, we can recommend some tips which can improve the Clarity' speed in certain situations:
1) Set the appropriate treshold.
2) Set the appropriate frequency of data acquisition.
3) Turn off the unused tables in Clarity (Performance, SST).
4) Turn off the Overlay function during the Sequence.
5) Turn off the PostRun Printing.
6) In your antivirus SW, turn off the option "Check Files at Change", especially for files used by Clarity (*.raw and *.audit).

The minimum Clarity's hardware requirments can be found at Compatibility page. Very helpful is often to increase the memory in the PC (RAM) rather then improve processor (CPU) speed.

Yes. Normalized % calculation is available in Clarity version 3.0 and newer. Use the NORM option in the Calculation tab of the Method Setup window. With this option set, Clarity automatically verfy:

• Sample Amount=0.
• All peaks in chromatogram are identified (calibrated).
• All peaks in calibration are also identified in the chromatogram.

In older versions of Clarity, use the Amount % column in the Chromatogram - Results table to get the Normalized % calculation. To get correct results, the user must ensure, that all peaks in the chromatogram are identified and calibrated. Remember that Clarity can be updated to newer version for free.

Symptoms

U-PAD2 with Windows 2000 will crash computer, when disconnected during analysis

Cause

There is a bug in the SiLib.sys file (a driver from Silabs) causing a crash of a computer when the hardware is disconnected during an operation. This bug will be probrably not fixed at Silabs, so we recommend to use newer version of Windows (XP, 7, ...) where this problem doesn't occur.

It is neccesary to set same desktop file (dsk) for all user's User Accounts.

How to:

1. Go to the main Clarity window, use System - User Accounts menu command.
2. Select the user with the desktop file already created and prepared.
3. Copy a filename from the Desktop File field to all other users:
   
   a) Select another user from User List.
   b) Paste the filename to the Desktop File field.
4. Repeat the steps 3a) and 3b) for all users in the list.

Agilent & HP Chemstation requires for import AIA files which are integrated (must have at least one integrated peak otherwise the import will not be performed), but not calibrated (set calculation to UNCAL before export, otherwise some of the released Chemstation versions may crash during import of such a file.)

The Event Table (especially the Output column) may be corrupted after changes in the instruments' configuration used in it or after some changes in PC's hardware. In such case, it is neccessary to adjust the Event Table.

The "No Data received for 10 sec" message means what is says, no data were received from a detector or convertor (U-PAD, etc.) for a certain period of time. That is in most cases caused by some problem on the computer - processor overload, interference on the USB bus, time consuming net search or backup operations blocking the communication for some time. The error invoked will cause interrupting of the sequence.

This will occur more frequently on slow computers, the triggering action may be processor overload or some programs blocking the communication for extended period. A prime suspects are programs checking the USB devices for media in the background (Adobe Acrobat, multimedia players, photo and image viewers, antivirus, ...). One such persisting problem was reportedly solved by removing the Roxio Burning software.

If you have an instrument with multiple detectors, they have to be configured on one Clarity Instrument only. That means they have to be started at one time and will use common time base.

The serial numbers of the workstation and protective key do not match. Use the Help - About command in the main Clarity window to check the serial number of the station (available in the Help - About dialog, Clarity tab).

The SST (System Suitability Test) module is dedicated to calculating of statistical parameters. This module is integrated in the Chromatogram window. This module can be purchased additionaly and is available as part number (p/n) A22.

There may be an error message hidden behind the splashscreen (picture). You can use the following  workaround:
Start the station with a parameter -hide_splash, this should reveal the  problem.

The easiest way is to modify the shortcut icon on the desktop - use  right mouse button on the icon to enter its properties page and add this  parameter after the "c:clarity liteclarity.exe" in the Target field.

If the problem persist, update the Clarity to newest version or contact suplier of your Clarity.

Find out what instruments (detectors, autosamplers, ...) are you using in your laboratory and what do you want to connect to Clarity. Contact one of our distributors or email us directly to sales@dataapex.com.

Our current INT9 and U-PAD2 A/D converters can acquire data at the maximum frequency 400 Hz, that means 400 samples per second. This frequency can be set up in the software. The older INT7 and U-PAD1 A/D converters can acquire data at the maximum frequency 100 Hz.

The serial number can be found in the About dialog.

1. Open the main Clarity window (or Clarity Lite window).
2. Use the Help - About menu command to invoke the About dialog.
3. Serial number can be found in the first tab.

You can also find it printed on your installation CD ROM or in the packing list.

A slowdown in the computer performance after installing the drivers for the Sentinel protective key may be caused by incorrect settings selected during the installation. These problems occur when Clarity is running and you try to work with files/directories on the network (for example, searching for the network printer).
Clarity installer correctly installs Sentinel drivers with disabled "Sentinel protection server" and "Sentinel Keys Server" options. However, if the drivers were previously installed manually, the options that cause the slowdown could have been set.

Solution:

• Run the Sentinel Protection Installer 7.3.2.exe program found in the HW_DRIVERSSENTINEL subdirectory on your Clarity CD
• Get to the "Custom Setup" dialog:
  - If Sentinel drivers are already installed on your computer, choose the "Modify" option in the first dialog.
  - In case you have no Sentinel drivers installed on your computer so far, select the "Custom installation" option during the installation.
• In the list of installed devices, disable the “Sentinel Protection Server” and “Sentinel Keys Server” options.

While installing Clarity version 2.5 on a PC with Windows Vista, where Clarity older than version 2.4.4.124 was previously installed, follow these steps:

1. Remove your protective key (Rockey or Sentinel).
2. In case of Rockey key, manually delete files rockey4.sys and rockey4usb.sys from the SYSTEM32DRIVERS subdirectory of your main Windows directory.
3. Restart your computer.
4. Uninstall the driver using the InstDrv.exe (in case of Rockey) program found in the HW_DRIVERSROCKEY subdirectory or Sentinel Protection Installer 7.3.2.exe (in case of Sentinel) program found in the HW_DRIVERSSENTINEL subdirectory on your Clarity CD.
5. Restart your computer.
6. Install the drivers by the same program (InstDrv.exe or Sentinel Protection Installer 7.3.2.exe, respectively).
7. Insert the protective key.

If you won’t follow these instructions, the crash of the system may happen. This is caused by persisting versions of Vista-incompatible Sentinel or Rockey drivers. To remedy possible problems, re-install the drivers according to the instructions given above.
Also, crash of Windows Vista may occur when the Rockey protective key is removed after an older version of Clarity was replaced by version 2.5. Again, in order to repair the trouble caused, do not insert the Rockey protective key back to the system and re-install the drivers as shown above.

If this will not help, contact our technical support.

There is known bug regarding the Windows XP servis pack 2 incompatibility with the earlier version of U-PAD driver, leading to BSOD (Blue Screen Of Death) when starting Clarity.

There are two possible remedies:

a) update Clarity software

• Download Clarity Full version
• If you have Clarity 2.3 and older - download the latest 2.3.x version from CLARITY PREVIOUS FULL VERSIONS section
  (update from this version to Clarity 2.4 and later would require to purchase HW Key (p/n C550) for manipulation fee.
• If you have Clarity 2.4. and later - download the latest available version from CLARITY FULL VERSIONS section
• Disconnect the U-PAD before installing the update.

The uninstallation of earlier version is also strongly recommended - use the Remove Clarity command from the Windows Start menu, Programs, Clarity program Group. This will remove the program components only, leaving your configuration and datafiles intact.

b) update only the U-PAD driver

• Download the updated U-PAD driver from Downloads - Others section
• Overwrite the existing cswupad.sys file in windowssystem32drivers directory with the downloaded file.

This happens usually when upgrading Clarity from earlier version. To get Passed for IQ result, it is necessary to remove the previous Clarity installation first using the "Remove" command from the Windows Start menu, Programs - Clarity program group. The IQ program checks all registered files and in case they are no more used in the new version, they will cause the check to fail. However, the station will usually function correctly. The Remove command will remove the program files only, leaving the configuration and data intact.

Clarity EVAL was renamed to Clarity Offline. It is because users often considered Clarity EVAL to be a kind of demo for Clarity software. Since it is a full featured product intended for working with data and preparing methods without the possibility to acquire data, the name "Clarity Offline" better reflects its purpose.

It is not possible to use them simultaneously. However it is possible to install both versions on the same computer and start them by a start_clarity.bat file. This bat file will re-register the dynamically linked libraries to the proper version.
You can download the Clarity-multiple-instances-on-a-single-computer.zip file with the start_clarity.bat and detailed description on how to use it.

N/A means not available, the Result table will display this when the computation does not make sense. For example if a calibration curve does not pass through zero, it can produce negative amount for given response, this is of course nonsense. Correcting the calibration curve fit will most probably fix this problem.

It is not posible even technically for the device to run on two independent timebases.
This problem applies generally to all Control modules. Some devices contain parts "subdevices", such as Signals in FLD that cannot cannot be used on two independent chromatography sets at once. It is usually not technically possible. The most recent Control modules will show a warning during the configuration procedure when you attempt to split indivisible device between multiple Clarity Instruments.

Yes, it can, however the philosophy of use is slightly different. The peak areas belonging to a selected group of peaks are summed and the group can be named and calibrated as a single compound. Please, see the corresponding parts of Reference and User guides. Especially in the calculation of Result table Total line and Amount % column are some potential problems, if the calculation procedure is not understood.

The injection volume used in the software is always in ml and could not be changed with the exception of Sequence table.

The overlay (Menu File, command Overlay mode) must be On to display several chromatograms simultaneously. The printing of chromatograms in overlay is governed by the options "Tilled by" selected in the Report setup, section Chromatogram. The options are Signals (each signal will be printed in separate box), Chromatogram (signals from one chromatogram only are overlaid, each chromatogram is printed in separate box), Not tilled (the overlayed chromatograms are printed as seen on screen).

A new project can be created (opened, changed..) in the current instrument directory only. However an arbitrary directory for each instrument can be set in the main Clarity window using the System - Directory command.

Possible causes are:
a) Detector not allocated to instrument:
- Open the System Configuration dialog from the main Clarity window and check the tab of the corresponding instrument Instrument x.
- In the left-hand Setup Control Modules list select the correct detector connected to the A/D card you are using and link it to the corresponding instrument on the right.
- If your A/D card is not in the left-hand Setup Control Modules list, add this using the Add button and repeat the previous steps

b) You have purchased a licence for data collection from a smaller number of instruments:
- Open the System Configuration dialog from the main Clarity window using the System - Configuration command and check the tab of the corresponding instrument – Instrument x. If the symbol of the curve in the tab header is blue, this concerns an instrument by which it is not possible to measure.
- Check your serial number S/N for example using the Help - About command from the main Clarity window.

If you only see the Demo caption in the header of the main Clarity window without any further description, you probably did not enter the user code of the workstation during installation. Use the Help – User Code menu in main Clarity window to enter the serial number of the station. You will find it on the installation CD or on the attached CD package inside one of the guides; if necessary, contact the manufacturer or your distributor to request this code.

The corresponding instrument displays only the simulated curve or has a so-called DEMO driver attached instead of the dataacquisition driver.

Yes, We will continue to provide updates free of charge. The latest versions of our software are available from our web page www.dataapex.com Users can also automatically update SW directly from their Clarity software.

Yes, upgrades are available. If users wish to upgrade to Clarity they have to buy an upgrade according to the current pricelist.
Have a look in the Product catalog, the upgrade options are listed there.

The customer can connect up to 4 instruments (chromatographs) to the Clarity Chromatography Station on one PC. Up to twelve detectors on 1 instrument, max. no of channels is 48 ( 12x4). PCs usually have 3-4 PCI slots. The user can also combine PCI A/D cards with the U-PAD/U-PAD2 (USB) and Net-PAD converters.

Users can load CSW32 files into Clarity software. The Save command automatically converts CSW32 data to the new “Clarity format”.

However, because of the new multi-detector measurement feature, users will need to edit the CSW32 method/calibration files in case he/she has an instrument with more than 1 detector. CSW32 uses a separate method for every detector. Clarity uses one method for the entire Instrument with up to four detectors.
For further details please refer to “Clarity vs. CSW32 Guide”.