FAQ

A Connect key is needed to activate communication between Clarity and Nexera control module. The Connect key (text file) will be generated by Shimadzu support upon providing the following numbers:
1. the Controller (CBM-40, SCL-40, CBM-40 Lite) Serial Number
2. the purchased RC.net Agilent ICF Nexera LC driver License Number (provided by us as a document based on the purchase of p/n A24-001 LC Shimadzu Control license).

No, there are not. CSW17/CSW32 software is discontinued from sale as of May 2004, it cannot be upgraded directly to Clarity any longer. Users have to purchase a new license for Clarity software.

No, it is not. Neither Clarity nor any of its components are using the log4j library. In fact, Clarity is not using Java at all, so this vulnerability does not apply to it.

Clarity stores the IP address of the device detected during autodetection in the configuration and if it changes, it is unable to communicate with the device. Some devices use IP adress assigned by DHCP server in default settings.

If the system is connected directly to the computer or via a switch, it is necessary to set static IP addresses in the devices and in the LAN card in the computer (preferred solution). Refer to the device manual or contact device manufacturer/supplier for how to change the device setting to a static IP address.

If the system is connected directly to the computer via router, it is possible to use DHCP IP address assignment, but you must ensure that the assigned IP addresses do not change. The same applies for connections via an internal network, where the cooperation of the network administrator is required to set the IP address.

The control of Shimadzu Nexis GC-2030 GC and Nexera LC-40 HPLC is available in Clarity - Shimadzu Edition (p/n C50-28).
It requires a Shimadzu license for each connected instrument p/n A23-001 for GC-2030 and A24-001 for Nexera HPLC Series.
Clarity - Shimadzu Edition is available only in Europe.

Examples:

Configuration for Clarity Shimadzu Edition with one Nexis GC:
p/n C50-28 Clarity Shimadzu Edition for 1 Instrument
p/n A23 GC control
p/n A23-001 GC Shimadzu license for one GC
optional:
p/n A26 AS control (in case there is a Clarity controlled autosampler)

Configuration for Clarity with two Nexera HPLCs:
p/n C50-28 Clarity Shimadzu Edition for 1 Instrument
p/n C55 Add on Instrument
p/n A24 LC control
p/n A24-001 LC Shimadzu license for one HPLC, 2x
optional:
p/n A26 AS control (in case there is a Clarity controlled autosampler)
p/n A29 PDA extension (in case Nexera includes a PDA detector)

Configuration for Clarity with one Nexis GC and one Nexera HPLC:
p/n C50-28 Clarity Shimadzu Edition for 1 Instrument
p/n C55 Add on Instrument
p/n A23 GC control
p/n A23-001 GC Shimadzu license for one GC
p/n A24 LC control
p/n A24-001 LC Shimadzu license for one HPLC
optional:
p/n A26 AS control (in case there is a Clarity controlled autosampler)
p/n A29 PDA extension (in case Nexera includes a PDA detector)

When ordering an upgrade from Clarity to Clarity Shimadzu Edition (p/n C620-28) do not forget to add a Shimadzu control license p/n A23-001 or A24-001.

Since Clarity version 8.0 and newer it is possible to print audit trail of method used for acquisition solely using Method Setup dialog. In case it is required to print audit trail of method (*.met) file it is necessary to perform this print directly from Method Setup dialog.

In case there will be requested print from different location (for example from Chromatogram window) with checked option 'Method Audit Trail' from tab 'Audit & Signatures' from Report Setup dialog nothing will be printed. This means it is not possible to print together with chromatogram an audit trail of method (*.met file) used for its acquisition, thus procedure described above has to be applied.

Yes, it is possible. The procedure is described in the Clarity Whitepaper How to capture network communication using Wireshark (Network Protocol Analyzer) (D142), please see the Whitepaper section to view the datasheet.

For Gow-Mac GC chromatograph use asymmetrical connection as shown on the picture below.

Connect Brown wire (Pink tubular end sleeve) to Terminal (+) and White wire (Grey tubular end sleeve) together with Yellow wire (shielding) to Terminal (-).

Do not connect anything to Terminal marked D on picture, it may cause the damage of the A/D converter.

Set also the Signal range at Method Setup Acquisition tab to the lowest possible value.

Yes, this is possible from Clarity version 4.0. In both the Sequence window and the Single Analysis dialog it is possible to define the name of the file including the subdirectory - use the \ sign in the name of the file.
It is possible to use the standard Clarity variables in the name of the subdirectory - the file name could look for example like this:

In the given example, %s\%q_%Q_%R is used for creating the file name, which means a subdirectory with the sequence name (%s) will be created in the working directory, inside of which the files with a name of SampleID_Sample_Date-and-Time format will be created.
If the folder is not present at the moment when the acquisition is run, it will be created automatically (you might be prompted to confirm the folder creation). If the subfolder is already present, the file will be created in it.

In this respect, please take care not to break Windows file and folder naming rules, so check that space will not be the last character in the folder name, etc.

This problem is caused by the wrong configuration file saved in Clarity\cfg. The most common reason is that the computer was shut down while Clarity was running. Normally, Clarity saves the clarity.cfg file when exiting, but 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. Here are the two most common situations:

• When the computer is switched off while the Clarity is running, e.g., while experiencing some fluctuations in the power system.
• When the computer is switched to the sleep mode, while Clarity is open, but not running (e.g. during lunchtime). While the analysis in Clarity is running, Clarity blocks switching to the Sleep mode, but without it, it can't do so. In sleep mode, the computer loses the communication between Clarity and the A/D converter and/or hardware key, which may result in destroying the configuration.

All data, such as methods, sequences, data files, calibrations, etc. are saved on demand and are not corrupted when a similar situation arises. The clarity.cfg file holds the information of the Directories and the System Configuration settings, that are lost, so they must be set manually once more.

To repair the damage, follow this process:

1. Open the System Configuration dialog and configure your system manually (eg. add detectors, LCs, GCs, valves and so on to the configuration), fill in their settings and distribute them to particular instruments.
2. Close the System Configuration dialog by clicking OK.
3. 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.
4. Open the Instrument. Load the desired project to the Instrument; Default clarity.cfg file has the 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.
   Note: You might get the information similar to "the current method was prepared on a different configuration. Some parameters will be used in default format" if you opened and then saved the method after the clarity.cfg file was corrupted, there might be necessary to check/set some parameters, mainly on the Method Setup - Acquisition and Method Setup - Measurement tabs.
5. Exit the station. The clarity.cfg file was now saved with the correct settings of the configuration.
6. You can back up this configuration to some other directory to prevent the manual settings if the problem occurs again.

The station should now be in the configuration as before the failure.

To prevent this from happening in the future if the reason was the sleep mode follow the procedure:

• In Windows 10 and 11 invoke Settings - System - Power & Sleep - Additional power settings - Choose when to turn off the display - Change advanced power settings and set Sleep after item and Hibernate after to "Never". Apply changes and use OK to exit this dialog.

• In Windows 7, 8.1 go to Control Panel - Hardware and Sound - Power Options - Edit Plan Settings to change the settings.

Corruption should be prevented in the future. Of course, if it was caused by another reason, such as instabilities in the power network, only a good stabilized backup power source and backing up your configuration may help.

Precondition:

The Retention indexes columns are hidden in the default layout of Clarity tables (Reten. Index in Clarity corresponds to Kovats Retention Index).
To display them in both the Calibration window and the Chromatogram window:

1. Open the Calibration (Chromatogram) window.
2. Point the 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 Show 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.

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.

The serial number and user code can be found in the About dialog.

1. Open the main 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.
4. Both user code and serial number can be found on the System files tab with other fundamental information about both the station and the computer.

You can also find it printed on a plastic card supplied to your USB installation media or it can be found in the packing list.

User privileges settings:

• Clarity (Lite) users must have read/write access to the Clarity system and data files. The default C:\Clarty (C:\Clarity_Lite) directory inherits the Read Only status from C:\ on administered systems. Contact your local administrator to change the settings.

Antivirus programs:

Antivirus programs usually do not interfere with Clarity functionality. But two areas may pose problems for the correct functioning of Clarity (Lite):

1. Antivirus is causing processor overload under certain situations which may leave insufficient memory resources for Clarity (Lite).
2. Antivirus is continuously monitoring files frequently updated by Clarity (Lite) (.raw, .audit, etc.) which may be unjustifiably marked as a threat to the PC.

Windows Updates:

Automatic Windows updates are in the default settings able to force the unattended computer to restart regardless of running programs - only a warning message will appear. Please note, that the first two options (Automatic updates or Download updates) may result in the forced computer restart.

Choose one of the options for automatic updates:

• Never check for updates.
• Check for updates but let me choose whether to download and install them.

On administered systems ask your local administrator to choose one of the options described above.

In Windows 10 and 11 it is not possible to forbid the updates, just to pause updates for short period of time and install them after manually to avoid forced restarts. Go to Settings - Windows Update - Advanced Options - Pause Updates

In Windows 7, 8.1 go to Control Panel - System and Security - Windows Update- Change settings.

We recommend installing and operating Clarity on a PC with updated OS, only the forced restarts pose a potential problem to Clarity.

Windows 8 and later may contain a predefined larger size of fonts than previous versions. It may also occur in Windows 7 when the user changes the font size.

Since Clarity version 7.2, the majority of problems caused by larger fonts have been resolved. Therefore update to the latest Clarity version should help. If not and Clarity is displaying apparently larger font, cut text or labels in table headers, etc., check the Windows settings. In Windows 10 invoke Settings - Display - section Scale and Layout. It is recommended to set the 100 % (default) option.

Warning message "Method xxx.met is modified and can not be sent. Save the method first and then send it" is displayed whenever user tries to send non-modified method from the Method Setup dialog. "MODIFIED" string is displayed repeatedly even after saving the method. Such behaviour was reported for selected ECOM modules. Possible workaround is to send method from elsewhere than the Method Setup dialog - i.e Data Acquisition or Device Monitor windows. The corresponding method need to be selected first in the Single Analysis dialog in the Method field manually.

List of error messages:

▌An unknown error occurred while accessing C:\Users\<user name>\AppData\Local\Temp\Clarity\$ch1run.raw

It can be displayed during the start of the acquisition, probably when the User does not have writing rights into C:\...\Clarity.

▌Attempted an unsupported operation.

It may occur when accessing a broken dialog or window. Please contact our support and describe in which window it happened.

▌Board malfunction

Probably there is an error in communication with DataApex converter. See a manual of INT7 or INT9 - chapter Troubleshooting, table List of Error Messages.

▌Blocked HW key

Your HW key has for some reason been blocked. Contact our support for help.

▌Cannot add device group

When trying to drag the whole group of devices (AS, GC, ...) over to the Instrument.

▌Cannot add some subdevices. - DEMO - 1 was configured on Instrument XX

If the number of DEMO detectors in configuration exceeds a certain number. Up to 10 is definitely still fine.

▌Cannot connect with communication library CswHP1100.dll. Install Agilent IO Library Suite version 15.

Libraries for GPIB are not installed (e.g. when switching the station from Clarity Demo mode with 1100 over GPIB in configuration). We do not include the libraries, see the Agilent website. Also note that GPIB communication is no longer supported since Windows 7.

▌Cannot create Detector

This error message can occur while using a DataApex A/D converter. Probably an unregistered library. Please contact our support.

▌Cannot create RAW file

Cannot create raw file C:\Users\<user name>\AppData\Local\Temp\Clarity\$ch1temp.raw is an error message which occurs due to very specific circumstances.

After starting the analysis, the file $ch1run.raw is created. When the analysis finishes, it is then renamed to $ch1last.raw from which the chromatogram *.prm is created. The file $ch1temp.raw gets created in case the renaming is not possible - usually due to a modal error message which awaits confirmation.

▌Cannot create temporary files

At Clarity startup if the user cannot write to C:\Clarity (installed without administrator rights).

▌Can't create ... (device name)

Usually a problem with the control module library (*.dll file). See FAQ - Question "I get an error message (Error on setup, Can't create ...) when I want to add an hardware to Clarity Configuration".

▌Cannot determine the number of bytes in input queue for Serial communication. System Error Information : 31. A device attached to the system is not functioning

If Multicom is unplugged from the USB of the PC (ECOM LCO connected over Multicom).

▌Cannot determine the number of bytes in input queue for Serial communication. System Error Information : 1167. The device is not connected

If Multicom is unplugged from the USB of the PC (ECOM LCO 102 connected over Multicom).

▌Cannot establish communication with XXXX SN xxx! XXXX SN xxx might not be connected, installed properly or it might be malfunctioning

In an attempt to open Instrument which has an uncommunicative device in configuration (e.g. unplugged U-PAD2 or Colibrick).

▌Cannot find driver file

From version 2.8 and later - this message pops up if an DataApex internal A/D (INT7, INT9) card is configured but physically unplugged. Also if the device is disabled in the Device Manager. See a manual of INT7 or INT9 - chapter Troubleshooting, table List of Error Messages.

▌Cannot find first board

This message may occur when a user wants to configure more A/D cards than is present in the PC.

▌Cannot find RAW file

This message has occurred while ending the analysis (Agilent 7890). Cause unknown yet.

▌Cannot find second board

If the user tries to add a second board which is, however, not present in the PC. See a manual of INT7 or INT9 - chapter Troubleshooting, table List of Error Messages.

▌Cannot load device driver

This message could have occurred on older versions of Clarity (for example on 2.5.6.99), probably due to a missing DataApex INT7 card. See a manual of INT7 or INT9 - chapter Problems with INT7.

▌Cannot load script xxx server execution failed (Ruby control modules)

Problem is caused by recent Windows 10 update (Build 1809), which is blocking the used RUBY script intepreter library version used due to a vulnerability issues. For remedy, please update to Clarity version 8.1 or higher, the affected library was updated in it.

▌Cannot open File Open Dialog. An unknown error occurred during this operation

This message seems to be related to exhausted Windows resources. Make sure you are using the latest version of Clarity and a fully functional Windows installation.

▌Cannot open file XXX The file is already open on Instrument YYY.

If you attempt to open a method that is already opened on another instrument.

▌Cannot open USB communication for XY

For example U-PAD2/Colibrick. Possible causes are if the A/D converter is connected over a USB hub or if there is a problem with DLL registration.

▌Cannot send data in serial communication

If you have, for example, a GC connected over a NetPAD and in configuration you first remove the NetPAD and then try to perform something with the GC.

▌Changing project requires to restart instrument. (You will be prompted to save modified files.) Is this OK ?

If you have unsaved changes in the Chromatogram window and you also want to change a project on the instrument.

▌Clarity is already running!

Appears during the startup of Clarity.exe if another instance is already running.

▌Clarity.psw file has been changed. Please see help file for possible reasons.

When upgrading Clarity from versions older than 8.0, this dialog may occur at first run and be logged in Station Audit Trail. It is a standard behavior caused by security improvements in newer versions of Clarity.

When manipulation with the *.psw file has been detected, it appears during the start of Clarity . This manipulation may mean a *.psw file from another station was copied to the Clarity configuration folder (C:\Clarity\Cfg by default) or when Clarity closed unexpectedly (Clarity crash, PC power failure, ...) when the *.psw file was modified but not yet saved.

When the *.psw file found does not contain a record about station running in the Regulated Environment, station will normally continue working and no message will be displayed on further Clarity station starts. If the *.psw file contains the record about station running in the Regulated Environment, station will not start at all. An empty *.psw file from the \Cfg\BACK\LAST_INSTALLATION\ subfolder can be used, all user accounts must be recreated and all GLP options must be re-selected.

▌Clarity.psw file has been corrupted. Clarity will now terminate. Replace the corrupted Clarity.psw file in Clarity folder (C:\Clarity\Cfg) with default file from the backup folder C:\Clarity\Cfg\Back\Last installation. All user accounts will be lost.

Appears during the start of Clarity when *.psw file is corrupted (illegible). Clarity will not start at all. An empty *.psw file from the \Cfg\BACK\LAST_INSTALLATION\ subfolder can be used, all user accounts must be recreated and all GLP options (if used) must be re-selected.

▌Configuration file C:\Clarity\Cfg\Clarity.CFG is not valid. The file was either damaged or created with a later version of the software. The backup copy will be used.

Appears when starting Clarity with a non-compatible *. cfg file.

▌Configuration file C:\Clarity\Cfg\Clarity.CFG is not valid. The file was either damaged or created with a later version of the software. Contact support for help.
Appears when starting Clarity with a non-compatible *. cfg file. Backup cannot be restored in this case.

▌Detector 1 (= NAME OF SIGNAL) is not acquiring any data

In case of high load on a low performance PC. This error may also occur due to physically damaged card during acquisition.

▌Encountered an improper argument

In version 3.0.3.295, this message appeared when the PDA tab in Report Setup was moved from the initial position.

▌Error Occurred During Setup.

This message can happen during the configuration of a control module.

▌Error 1008 V-2500 (Upchurch) (SN N/A): Not Connected

If the valve from a COM port is disconnected, it is switched from Waiting to Communication Error.

▌FAILED to send method to device (Thermostats)

When thermostat is unplugged from RS232 and then "Send Method" is pressed manually.

▌FAILED to send method to sub-device

If the device stops communicating with several parts (e.g. 7890).

▌Fraction table contains overlapping time intervals. Please amend the table so that the time intervals don't overlap.

This error occurs if the user creates a wrong table for a fraction collector with overlapping times. It is a warning for the user that the fraction table needs to be corrected in order to avoid presence of the overlapping time segments in the table.

▌HW Key test Failed

Your HW key is not working correctly. Contact our support for help.

▌Incompatible device driver

The kernel driver and the driver in the Clarity do not match.

▌Invalid rows detected in the Method Setup - Event Table. The invalid rows will be marked out and skipped from events processing

This message appears during the opening of a method whose Event Table uses something that is not in the configuration.

▌Method file XXX does not exist. For more information about errors on the other rows, point mouse cursor over "Sts." Column for each row.

This happens when opening or checking a sequence which contains a name of a non-existent method.

▌Method file XXX was prepared with different instrument configuration and cannot be sent into HW. Open Edit Method Dialog and press OK to adapt it to the new configuration (non-matching parameters will be replaced by defaults).

If the instrument or method being opened does not correspond to the hardware which is currently present in the configuration.

▌Missing keylock drivers

The drivers for the HW key are missing or corrupted. They need to be reinstalled. See FAQ on our website - HW key (re)installation.

▌Net-PAD (SN Error) Cannot send sockets.

Net-PAD is not communicating. This may be due to a faulty cable or that when using a direct connection the PC does not have a static IP address set up.

▌NETPAD malfunction

This message appears if the data do not arrive within 7.5 seconds.

▌No data received for 10 s.

This message may occur during an acquisition if Clarity has not received any data for a prolonged period of time. Make sure the PC is not under high load during the acquisition.

▌No detector has been found and not even DEMO detector has been found

The control modules may be incorrectly registered. Please check the IQ Report of Clarity.

▌Please enter valid Data Size. Minimum is 2.

The content of the imported file is too short (only one data point on the graph).

▌Project directory <Project name> already exists but has no project file! Do you want to create the project file?

Project directory with this name already exists but it misses its project *.prj file. Select one of options. It is recommended to select Yes option.

▌Project file <Project name> already exists but has no project directory! Do you want to create the project directory?

There already exists project *.prj file with given name but it misses its project folder. Select one of options. It is recommended to select Yes option.

▌Project <Project name> already exists! Choose a different name.

Project with this name already exists. Select another and unique name for newly created project.

▌Seek failed on C:\..... .csv

The content of the imported file is too short (less than 5000 Bytes). Please update to the latest version of Clarity.

▌Shutdown from Event Table

This message appears after executing the Shutdown command from the Event Table.

▌Stop time must be larger than Start time for individual fractions.

This message concerns fraction collectors. The Fraction table contains incorrect settings of Start Time and Stop Time for one or more rows. Each row of the Fraction table has to be set such that the Stop Time is always higher than the Start Time on the same row.

▌The directory specified for instrument x does not exist: C:\...... It is necessary to set correct directory with projects for instrument x in Directories dialog.

This message appears during the opening of an Instrument window while deleting/renaming or damaging the respective directory in the meantime.

▌The installation of Microsoft Visual C++ 2005 Redistributable Package (x86) failed. Exit code: 1618 Installation of Windows update or another program is already in progress. Let it finish first, restart the PC if necessary, and then start Clarity installation again.

This can happen when Windows update or another program is already being installed, in rare cases, this is caused by the Windows installer process not being terminated properly. Waiting for the installation to finish and restarting the PC should resolve the issue.
 

▌The report style "Chromatogram.sty" does not exist or is damaged. Default report style "Noname" will be used instead.

This message appears during the opening of a Chromatogram window while deleting/renaming or damaging the respective .sty file in the meantime.

▌Too many peaks in chromatogram. Try to increase peak width or threshold

Peak Width was set to a low value (e.g. to 0.001 minutes in a 80 minute noise chromatogram).

▌Too much data for FFT. Max. number of samples in interval is 2E6

FFT applied to a too large interval.

▌Unable to lock instrument in unprotected mode!

When no user is created and you attempt to set Lock on an opened instrument.

▌UPAD (SN...): Cannot send data in USB communication.

For example when you unplug a USB cable during acquisition and confirm the displayed error, the Instrument then switches to a Communication Error.

▌UPAD device malfunction

This appears during the test of a UPAD when it does not provide any data. In other words, during the start of Clarity an acquisition signal 10V/100Hz is sent to the first UPAD channel and if there is nothing received from the UPAD in 1 second, this error message appears. See the manual of UPAD - chapter Troubleshooting.

▌User accounts file load error

The file Clarity.psw failed to load. Happens, for example, if you downgrade from 3.0 to 2.8 and leave the old files in place.

▌You are attempting to paste incompatible or out of range values

This message may occur while copying a sequence table prepared in Excel. Make sure the form of the table and its values are correct.

▌You entered 3 times wrong password, you must restart program

If the user submits a wrong password three times in a row prior to closing Clarity.

Error messages in IQ report:

▌Wrong checksum (size), probably different version of the file

Check the IQ Report to see if the Clarity installation is correct.

▌Warning: unknown control module

Happens e.g. in Clarity Lite for drivers of control modules if the PC finds a full version of Clarity installed.

▌Failed: bad size

The file has a different size (compared to iq.chk) - occurs e.g. in Clarity Full for .dll from Lite, if that one was the last registered.

▌Failed: bad checksum

The file has a different checksum (compared to iq.chk) - occurs for .dll which has the right size, but the checksum does not match. For example if you edit the size of iq.chk manually.

It was observed that an update from Clarity version 7.3 to version 7.4 may cause problems in User Columns‘ functionality. It concerns User Columns in the Summary Table of Chromatogram Window. After updating the station, the User Columns calculated values may disappear, the calculations by initial formulas might be incorrect or values can change when moving the order of the columns in Summary Columns Setup up or down, etc.

The reason for this is that the User Columns defined in desktops created in version 7.3 and older could not be restored correctly as the respective info was not stored (the columns were referenced to the current layout, not to the column ID).

This strange behaviour can be fixed when you right-click above Summary Table and select Restore Default Columns item. Then create the same User Columns with the same formulas again.

Clarity installation requires a specific version of Microsoft .NET Framework, which may not be installed or enabled on the computer by default. You will be notified by the Clarity installer which version of .NET is missing on your PC.

Some external control modules and their components may also require different version, which is not controlled by the Clarity installer.

There are three ways to obtain required versions of .NET framework:

• Install the version of .NET supplied on the installation media, folder dotNet.
• Download the version of .NET from the internet, using the links below, and then install it.
• Turn on windows updates to download the latest version.

Required versions of .NET Framework

• Clarity installation requires a version of .NET Framework 4.7.2 or higher
• Installation Qualification for Knauer HPLC requires .NET Framework 3.5 SP1

.NET Framework installation

On Windows 7, download the respective versions using the link below:

Click here to download .NET 3.5 SP1

Click here to download .NET 4.8 (this includes all previous 4.X versions)

On Windows 8.1, 10 and 11 follow these steps:

• Go to Start Menu –> Control Panel –> Programs and Features –> Turn Windows features on or off. (Or in the Run dialog enter "optionalfeatures".)
• In the displayed Windows Features dialog, check the .NET Framework 3.5 (includes .NET 2.0 and 3.0) and .NET Framework 4.X.

• Click OK and the selected option will be installed and enabled.

Note:
Installing .NET framework may require additional windows updates. Always follow the instructions supplied with each version of .NET you are installing. It contains information about additional updates and security fixes.
Installation of .NET 3.5 is not always smooth in Windows 10, consult with your IT to find the best way to install it.

In case you were asked for a User Code (U/C) during the update to Clarity 7.2, it means that the update has not been performed correctly. However, there is a simple solution.

1. Finish Clarity installation first - skip the step where you are asked to supply the User Code.
2. After Clarity is installed, do not start it.
3. Go to the installation directory of Clarity - this is by default in the C:\Clarity directory.
   It is highly probable that the installation directory will contain extra files and/or directories that were not intended.
4. The structure in the root Clarity directory should be exactly like the list below:
   • Bin
   • Cfg
   • DataFiles
   • uninstall.dat
   • Uninstall.exe
5. Move any extra project directory (which contains your measured chromatograms, calibrations, methods and so on) to the DataFiles directory.
6. Move any extra Clarity file (such as Clarity.dsk, Clarity.sno, Clarity.snp, Clarity.psw or similar) to the Cfg directory.
7. Finally, start Clarity and now it should not ask for User Code.

If you manually copy a control module *.dll (i.e. not using an installer) you have to run the regsvr32.exe with administrator rights to register it.

• Hit the Windows Start button or key on your keyboard, and type cmd in the search field.
• Right-click to open the pop-up menu and select Run as administrator.
• In the command line, type regsvr32.exe and a path to the .dll (for example "regsvr32.exe C:\Clarity\Bin\MyFile.dll") and press Enter. The library will be registered.
• If you will not perform the operation with the administrator privileges, an error message with code 0x8002801c will appear.

Since Clarity version 8.2. unauthorized control modules cannot be added this way.

Clarity is available in English, Chinese, Spanish, German, French and Russian localizations.

In Clarity version 7.0 a new organisation of the installation folder structure has been implemented to separate the program files (*.dll, *.chm), configuration settings (*.ini, *.cfg) and the user data (*.prj, *.cal).

During the update, the installation wizard will automatically move files to new locations. Once this is performed, it is not easy to revert to the previous version (i.e Clarity 6.2).

Suppose that you have Clarity version 6.2 and you want to update to Clarity 7.0. To make sure that you can revert any time after updating to Clarity 7.0, perform the following steps:

1. Make a backup of your projects, chromatograms, etc.
2. Uninstall the current Clarity version (6.2).
3. Start the installer of Clarity 7.0 or higher.
   1. Change the Destination Folder to C:\Clarity7 or other.
      (Otherwise, it would be installed over the previous installation.)
      
   2. Set data location to C:\Clarity7\DataFiles.
      
   3. Finish the installation.
4. To preserve your original configuration, copy the following configuration files from the original installation (6.2) to the new installation (7.0) CFG subfolder:
   1. Clarity.cfg (and potentially any other *.cfg files)
   2. Clarity.dsk (and potentially any other *.dsk files)
   3. Clarity.sno
   4. Clarity.psw

Reverting to previous Clarity

When revert is needed, perform the following steps:

1. Uninstall the new version (7.0)
2. Install the previous version to the original installation folder (C:\Clarity). The one used before the update to 7.0

If you already updated to version 7.0 in the same directory as you have installed the previous 6.2 version and did not make a backup of the previous directory, you can revert using this procedure:

1. Install Clarity 6.2 to the new directory
2. Manually copy the configuration files (*.cfg, Clarity.sno, Clarity.psw)
3. Transfer the projects with all the data by preferably using Archive/Restore commands, simply copying them to the Clarity folder can pose some risks.

Note that once you update to Clarity 7.0, Desktop files (*.dsk) are not compatible with previous versions of Clarity (6.2)!

The Clarity software license is fixed on the HW key. The software itself could be installed freely on different computers, but without the HW key, it will not start.

For moving Clarity to a new PC follow these steps:
1) Install the software on a new computer (the latest version could be downloaded from our website www.dataapex.com, section Downloads), you need to be registered and logged in. During the installation make sure all necessary drivers and control modules are installed - some may not be included in the Typical installation.
2) Connect the hardware (MultiCOM, A/D Converter, etc.) and the HW key.
3) Enter the user code matching the HW key.
4) To restore your settings copy the system files (clarity.cfg, clarity.dsk, clarity.psw) from the old computer to the Clarity\cfg folder on the new PC.

If you have Clarity Full version:
5) To restore the data, use Archive/Restore command to copy the needed projects (recommended procedure) or copy the respective folders (including the Projects and Common).

If you have Clarity Lite:
5) To restore the data, copy the respective folders (including the Projects and Common).

For one or more devices requiring the serial (COM) RS232 port, use the reliable MultiCOM adapter from DataApex (p/n MC01). Proper operation of the MultiCOM adapter has been approved by many of our satisfied customers.

If you purchase the USB to serial (COM) RS232 cable adapter from another manufacturer consider the following recommendations:

• DataApex strongly recommends NOT TO purchase USB-RS232 cable converters based on processor chips provided by Prolific. Prolific processor chips are known to be unreliable. The preferred chip manufacturers are Silicon Labs or Future Technology Devices International Limited.
• It is also strongly recommended to install appropriate drivers for these chips.
• When purchasing cable devices it is also necessary to consider limitations related to maximum cable length.

1. In the Agilent GC instrument, disable one of the analog outputs and on the used one, set the appropriate detector (front or back) you want to measure from.
2. Connect the analog output of the GC to Colibrick or one of our other A/D converters. See the hardware manuals at Downloads.

In case you have Clarity:

3. Add the Colibrick or one of our other A/D converters to the System Configuration and add the detector on the Instrument. See the hardware manuals for more details.

In case you have Clarity Lite:

3. After the start of Clarity Lite, you can start acquiring data immediately.

Since Clarity version 6.0, Clarity Demo is a standalone application. Functions of the Clarity Demo remain unchanged. To upgrade from Clarity Demo to the full version of Clarity, it is required to download the full version from www.dataapex.com in the download section or obtain it from your local distributor.

If you only see the red stripe inscription "DEMO - WRONG S/N" or "DEMO - Wrong User Code" in the main Clarity (prior to 6.0), the user code entered into Clarity does not match with the HW key. Use the Help - User Code command in the main Clarity (Lite) window to check the user code of the station.

Normally, drivers for MultiCOM are installed without any problems when the Typical installation of Clarity is performed from Clarity version 8.1, before that MultiCOM drivers were installed only during Full installation or when manually checked during the installation. Nevertheless on Windows 8.1 drivers for MultiCOM may not be installed properly. In such case, the following error appears: "Windows found driver for your device but encountered an error while attempting to install it. The system cannot find the path specified."

There are two ways to rectify this situation:

1. Reinstall the drivers manually. The process is described in the Troubleshooting section of the MultiCOM Manual.
2. If the first solution does not work then the problem may be on the computer side. A possible way to solve this issue is to restore the system, perform updates and uninstall some of the ‘bonus’ (spyware, online help utilities, etc.) software. After that reinstall Clarity and connect MultiCOM again.

Yes, Clarity natively supports the work with multiple ISTDs from version 5.0. Up to 10 internal standards are supported since Clarity version 8.0.

If you installed Clarity 5.0.2.612, you may experience a stability issue when using the Knauer PDA detector. Also, the existing methods are not compatible with the driver in 5.0.2.612 and will display an error. 

In case you need to keep the installation of Clarity 5.0.2.612, please download and install the provided hotfix, then start Clarity and create a new PDA method in the Instrument window.

In case you are able to update Clarity, please download the latest version from Downloads.

Clarity is fully supported on Windows 7, 8.1, 10 and 11. For more details see the Clarity compatibility table.

You can upgrade to the latest Clarity version for free at Downloads.

RkUSB HW keys may not work properly on computers with "AMD USB Audio Driver Filter" installed. It is recommended to check the driver details of RkUSB in Device Manager. In case a "usbfilter.sys" is listed, uninstall the "AMD USB Audio Driver Filter" driver from Windows using the "Add or Remove Programs" function in Windows. For more details see the support pages of your PC's manufacturer.

Yes, it is. Simply take your HW key and plug it into another PC. You can install Clarity (Lite, Offline) on as many PC as you like using the same user code. Clarity will work properly on the one PC with the HW key connected.

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

Note that Colibrick/U-PAD2 is sensitive to communication delays. Responsible for those delays in 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 than 10 seconds, an error will be invoked. Error messages "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 is interrupted. In case the problem is temporary, sending the method again may solve the problem. If not, disconnect and reconnect the USB hub.

Try the Task Manager and inspect the processor load and processes consuming a 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 disabled for scans. Any other programs monitoring files on exchangeable media (i.e. programs for organizing and presenting 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 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.

The above-mentioned problem with communication with Colibrick/U-PAD2 was not observed when the USB hub is connected to the USB C connector on the PC.

Yes, you can. There are two possible intentions of using the sequence table for starting the acquisition:

1. Using sequence for manual injections
   You could define parameters for a series of injections in advance in a sequence table and then inject them one by one manually. In such case, the start must be external (individual runs in sequence cannot be started from Clarity). 
2. Using sequence for automatic injections without an autosampler
   In such case, the sequence must be in the active mode (set through Sequence Options dialog). Sequence sends a command to the sampler (over a serial line or by digital output) and waits for the start signal from the detector (again over the communication line or digital input). Without an autosampler, it is possible to start the acquisition by using the digital input and output specified in Ext. Start Dig. Input and Ready Dig. Output section of the System Configuration dialog.

How to set digital input and output to start the sequence without an autosampler?

• 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 the DataApex's 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 a controlled valve, the injection is then performed during the actual run by switching the valve (or valves) from the Clarity Event Table.

Events must be set in the Event Table accessible from the Method Setup dialog.

• 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).

For more detailed info refer also to Clarity Getting Started manual, chap. 6.

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.

In case the computer is connected to the Internet, just select the menu Help - Check for Updates in the Clarity main window. The new version will be offered. You may need to fill in the registration form and proceed with selecting the default options suggested.

• For Windows 7, you need to install a Microsoft .NET Framework 4.7.2 or higher before running the Clarity update. Use the link below:

Click here to download .NET 4.8 (this includes all previous 4.X versions)

• For Windows 10, make sure you have installed all available Windows updates before running the Clarity update.

Alternatively, you could download the version from our web pages, section downloads - full versions. You need to register (including the S/N of the station) and login, then download the update, transport it (by USB flash disc) to the PC with Clarity and run the file.

These problems may occur during the setup of hardware (Colibrick, Int7, Int9, U-PAD2, ...) or controlled devices in the Clarity Configuration.

Error on setup

This error message means the problems are on a low level, either with a kernel driver or hardware itself.

Can't create ... (device name)

This error message usually points out the 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.dll version than the Clarity.exe

To solve this, uninstall the previous version of Clarity and then install Clarity again. Follow the chapter for reinstallation in the device's manual. Alternatively, it is possible to register the corresponding *.dll file using the Windows\system32\resvr3.exe program.

For preparative purposes, multiposition valves 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 usually necessary 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.

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 a new one, rewritten, etc.).

You can find the real acquisition date of the chromatogram in:

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

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 for Windows Vista/7 (Windows Vista OS is supported until version 7.2)
  • 4.0.4 for Windows 8 
  • 6.2 for Windows 10
  • 8.7 for Windows 11 (Windows 11 OS is 64-bit version only)

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 the 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 the 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. The driver was discontinued in version 8.7 due to the incompatibility with the supported OS.

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

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

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.

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

• Analog acquisition in modern detectors is realized by the following chain: analog detector unit, detector A/D converter, detector processing unit, detector D/A converter, analog cable, Clarity A/D converter (Colibrick, U-PAD2, INT9, etc.).
• The digital acquisition chain is much simpler: analog detector unit, detector A/D converter, detector processing unit, digital cable (USB, RS232, etc.), Clarity Control Module.

You can see at least three sources of problem in analog way:

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

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

• Quality of detector D/A converter (analog output resolution may be worse than digital).
• Length and quality of analog cable.
• Proper cable connection (symmetrical, non-symmetrical).
• The absolute level of the analog 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 Colibrick 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?

When running Clarity on a very slow PC or laptop, we can recommend some tips which can improve the speed of Clarity in certain situations:
1) Set the appropriate threshold.
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 requirements can be found on the Compatibility page. Often it is very helpful to increase the memory in the PC (RAM) rather than improve processor (CPU) speed.

Installation of the INT7/INT9 card driver is not part of the installation of the Clarity.

Install the Clarity before you plug in the INT7/INT9 card and switch off the computer. Insert the INT7/INT9 card and start the computer. Windows should automatically recognize the new plug, play the device and attempt to install the driver.

For complex help and troubleshooting see the INT7 or INT9 converter manuals, chapter Troubleshooting.

When 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 HW key (Rockey or Sentinel).
2. In case of the 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 the Rockey key) program found in the HW_DRIVERSROCKEY subdirectory or Sentinel Protection Installer 7.3.2.exe (in case of the Sentinel key) program found in the HW_DRIVERSSENTINEL subdirectory on your Clarity installation media.
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 HW 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, the crash of Windows Vista may occur when the Rockey HW key is removed after an older version of Clarity was replaced by version 2.5. Again, to repair the trouble caused, do not insert the Rockey HW key back to the PC and re-install the drivers as shown above.

If this will not help, contact our technical support.

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 "Tiled by" selected in the Report setup, section Chromatogram. The options are Signals (each signal will be printed in a separate box), Chromatogram (signals from one chromatogram only are overlayed, each chromatogram is printed in a separate box), and not Tiled (the overlayed chromatograms are printed as seen on screen).

The corresponding instrument displays only the simulated curve or has a so-called DEMO detector driver allocated instead of the data acquisition driver. Meaning that the signal is not real but simulated from a data file. The reason for the watermark "Simulated" could be one of the following:

• Either you have a demo detector allocated on that instrument. Check your configuration, remove the demo detector and allocate the needed control module.
• You might have installed the Clarity Demo version which does not allow real-time acquisition. Go to our download section and download a full version. Note that you need to be registered with the S/N of the station and during installation, you will need to insert a correct User code, otherwise Clarity will not start.

Yes, for this upgrade the part number (p/n) C540 is available.

Yes, we provide all Clarity updates free of charge. You just need to be registered before downloading. The latest version of our software is available from our web page in the download section. Users can also automatically update SW directly from their Clarity station using the Check for updates... command in the Help menu.