FAQ

You can read your software version from the software main window in the Help – About menu.

If you purchase a software upgrade for your Clarity or Clarity Lite Software license, you will get a free upgrade for your associated free Clarity Offline. You only need to list the Clarity Offline S/N on your purchase order as well. An educational discount also applies to software upgrades.

Yes, if you have registered your Clarity (Lite) at the DataApex website, we will automatically send you the new user code when a major version is released. You will receive an email with a new user code to the email address used in your registration.

There may be multiple different reasons. Please check the detailed status in the Instrument window and Device Monitor.

1. Waiting for Injection - indicates parameters for injection were sent to the sampler, but the start signal has not yet been received.
   Suppose the sampler is not working on the injection. In that case, it may indicate wrong synchronization settings in the System Configuration or that the start signal was not received or ignored for some reason.
2. Waiting for Hardware to be Ready to Run - indicates some of the devices configured on the instrument do not report Ready state.
   Check the status reported by individual devices in the Device Monitor.
3. Sequence Paused - indicates the sequence was paused.
   An automatic pause may happen if an invalid value is entered during the editing of the running sequence to prevent locking a line with an invalid value. After correcting the value, the sequence must be manually resumed.

Bar code scanner support is implemented within a few autosampler control modules (Spark Integrity, HTA HT4000, …). The read bar code will be available as the %f variable for use in SampleID, Sample, or Filename fields.

Hand-held scanners (emulating keyboard) could be used to fill in the values in the sequence table – the terminating character should be set to Enter, and the setting in the User Options dialog - General tab - Sequence Table - On Enter section should be set to Move Down option to move the focus to the next row after the Bar code value is read. 

For versions before 9.0, the option to set the terminating character to Down Arrow in the scanner will be advantageous; otherwise, moving to the next row using the mouse/keyboard is necessary.

In such case, it is recommended to check Colibrick Setup in the System Configuration window. Synchronize Start with Digital Input should only be enabled when one of Colibrick's digital inputs is configured as Exr. Start Dig. Input:. Furthermore, Synchronize Start with Digital Input and Exr. Start Dig. Input: must be set to the same Digital Input.
This change was made because the wrong setting led to random issues with analysis starts in previous versions.

Synchronize Start with Digital Input enables a faster and more accurate synchronization of channels with the start signal. The start of the analysis is defined by a marker in data points rather than by detecting the change in Digital Input. The difference is in the order of hundreds of milliseconds, which means that it is important only for very short analysis. When measuring multi-detector chromatograms it will minimize the time shift between detector signals and thus improve the detection of peaks.

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.

For the Gow-Mac GC chromatograph, use the asymmetrical connection as shown in 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 the terminal marked D in the picture, it may cause damage to the A/D converter. Set also the Signal Range at the Method Setup Acquisition tab to the lowest possible value.

The error message pops up after the start of Clarity.

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.

During acquisition, data are stored in the temporary directory (...\TMP\ $ch1run.raw file ). The data are stored from memory to disk in approximately 1 min intervals. In case the Clarity crashes/freezes during a run, the up to that moment acquired data could be recovered using the Data Recovery ...  command from the Single Analysis window. Note the chromatogram will be created according to the method and parameters specified in the Single analysis (file name and processing parameters), which may be different from the ones used in the Sequence.

During the freeze, it will depend if the thread collecting and storing the data to disk will be still active, with a crash, the data to the last minute before the crash could usually be recovered. In case the computer freezes often, it will be advisable to investigate the cause and try to find a remedy – please do not hesitate to send us the respective diagnostic files. A Memory dump may be helpful for such situation.

If your PC and chromatograph are connected directly via LAN and autodetect is not possible, continue with the following procedure:

• You need a cross-over ethernet cable (a straight-through cable is not recommended).
• Open Windows Settings - Network & Internet - Ethernet tab - Change adapter options - right mouse click on the Local Area Connection and choose Properties.
• In the Local Area Connection Properties, choose Internet Protocol Version 4 and click the Properties button.
• Check the radio button in the Internet Protocol Version 4 (TCP/IPv4) Properties window. Use the following IP address.
• Fill in the IP address. 
  • The first three positions define the network and must be the same as in the device's IP address. 
  • The last position defines the device and must be unique within the network, so do not use one of the connected instruments. Eventually, other Ethernet boards within the computer must not share the same network.
• The subnet mask needs to be 255.255.255.0

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

When Clarity (Lite) is started, an error message stating "Missing HW key" may appear. This issue arises when the required hardware key is not detected by the system.

If you encounter any problems, the first step is to check the USB port the key is plugged into. Try moving the HW key into a different USB port on the PC or another PC. Most issues are related to the USB port's energy-saving settings in Windows or a faulty USB port.

The Rockey USB ND does not require any separate driver installation; once plugged into a USB port, all necessary drivers are automatically installed. For problems encountered in the case of older keys, see the section below.

Make sure that the LED diode in the key is steadily lit. If it is blinking or it is not lit at all, the hardware key may be faulty, and you will need to send it to us for inspection. Please contact us at sales@dataapex.com in such case.

Old HW key types

The older HW key types require drivers to be installed prior to their use. The Rockey USB/LPT and Sentinel USB/LPT HW keys might not be functional due to installation of a wrong driver. This situation occurs in the case this HW key was connected to the PC before the installation of the correct driver by Clarity. This can be solved by manually uninstalling the wrong driver, restarting the PC, and installing the correct one. To do so, the installer of the drivers can be found in the Clarity\BIN\HW_DRIVERS\ subfolder.

Sentinel HW keys cannot be used with the current Clarity release.

Rockey USB	Rockey LPT	Sentinel USB	Sentinel LPT
	Rockey LPT key can be used only with LPT1 only on board LPT ports, not the ports on PCI cards

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.

To move Clarity to a new PC, follow these steps:

1. Install the software on a new computer (the latest version can be downloaded from our website, www.dataapex.com, section Downloads; you need to be registered and logged in). During the installation, ensure 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 the Archive/Restore command to copy the needed projects or 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 computers that do not have (enough) serial ports, we offer the MultiCOM device (6× RS232 to USB converter). Ensure you have a USB port in your computer to accommodate the MultiCOM.

Dani Master GC

In case your Master GC has an older firmware that supports an older version of Clarity than you have installed it is possible to use older drivers in newer Clarity (up to 8.1). Proceed as follows:

• Copy CswDaniSpAMasterGC.dll and MasterGCControl.dll from the previous Clarity version and rewrite them in your current Clarity installation directory.

It is not possible with Clarity version 8.2 and newer because of our internal policy.

Dani Master DHS

Dani Master SHS

The "No Data received for 10 sec" or "No data from Acquisition..." messages mean what they say, no data were received from a detector or A/D converter (Colibrick, etc.) for a certain time. It may be caused by several cases:

1. In most cases, there is 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 stop an acquisition or interrupt the sequence.
   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 pictures, music, or video, including some CD/DVD burning programs). One such persisting problem was reportedly solved by removing the Roxio Burning software.
   This will occur more frequently on slow computers, the triggering action may be processor overload or some programs blocking the communication for an extended period.
    
2. In some cases, Windows may suspend the power of the USB HUB in the computer and this unexceptionally causes a loss of connection to connected HW (e.g., Colibrick). Try to check the Device Manager dialog - Universal Serial Bus controllers. Display the Generic USB HUB Properties dialog - Power Management tab. Set Disabled for option Allow the computer to turn off this device to safe power. In case the problem is temporary, sending the method again may solve the problem. If not, disconnect and reconnect the USB HUB.
   The above-mentioned problem with communication was not observed when the USB hub is connected to the USB C connector on the PC.

State of Clarity Instrument can be read by other software using a built-in DDE server. For more information, please see the datasheet D070 DDE synchronization of Clarity with other programs.

If you add a User Column to both the Summary and Result Table containing the same formula, often you cannot get the same results. You cannot use the First, Last, etc. functions from Special Values in the Summary Table. 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]".

It is possible to schedule a task that will run Clarity with defined parameters automatically starting a sequence. Proceed as follows:

1. 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_304\Bin\Clarity.exe i=2 u="Administrator" psw="" seq=C:\Clarity_Demo_304\FC\FC3.seq run_seq=2

   Explanations:

   • start C:\Clarity.exe will start the Clarity in the specified directory
   • i=2 will open the desired instrument (2)
   • u="Administrator" psw="" will open it as a specified user with a specified password (essential, otherwise it stay waiting for this input)
   • seq=C:\Clarity_Demo_304\FC\FC3.seq specifies the sequence to run
   • run_seq=2 starts the sequence on instrument 2
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.
3. Use the Task Scheduler
   Set the clarity.bat to be started at a defined time and date. Open the "Task Scheduler" Windows app. Use the advanced properties of the task to fine-tune the scheduling.
   Set the task to start when you are logged on only, and when leaving the PC, do not log yourself off. Remember, Windows Update must not run there. It may log you out and restart the PC.

The path in the batch file can differ according to Clarity version you use (version up to 6.2 - start C:\Clarity_Demo_304\Clarity.exe i=2 u="Administrator" psw="" seq=C:\Clarity_Demo_304\FC\FC3.seq run_seq=2).

LAN communication

General issues

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

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

We don't support J4100A JetDirect card (alternative to HP JetDirect Print Servers 600N/400N/500X/300X) nor guarantee the functionality.

Connecting single PC directly with 1100/1200 system

In case you need to connect the PC directly with the 1100/1200 system using a LAN card, see chapter 3.3.4 Single PC & network connection in the Agilent 1100 manual.

GPIB Communication

Communication using GP-IB card could not be established

When the communication with the Agilent 1100/1200 system by the GP-IB card could not be established, even if all the parameters are set correctly and the Agilent IO Libraries report the module as connected on the used ID address, then it is necessary to check the Agilent IO Libraries.

The Agilent IO Libraries must be closed (Use the Exit command) before the communication with Clarity can be established.

During the installation of the Agilent IO Libraries, they are added to the programs to be started automatically at the system start. It is necessary to disable this function because they could not run simultaneously with Clarity.

• In Windows XP, Vista and 7 - remove them from the  Windows Start menu, Programs (All Programs), and Startup group.
• In Windows 8, 10 and 11 - start the Task Manager (display more details in the window) and locate the Start-up tab. Disable them.

After the communication was lost, it could not be reestablished

When using the GP-IB USB converter, it may be necessary to disconnect the converter from the PC to clear the communication buffers. As the USB can be powered even during a computer shutdown, the shutdown and restart may not help.

Most chromatography systems use a proprietary data format (the main reason is the 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 into a suitable format. The most commonly used formats are AIA (.cdf files) or ASCII (.csv, *.txt, *.asc, and others). Clarity can import such files (only the chromatogram data, not the integration method or result tables) and process them using the current instrument method.

Chemstation

• The export is available with full menus active in the 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), the 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 that 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.

Multiposition valves are frequently used as a simple fraction collector for preparative purposes.

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

To use valves for this purpose in Clarity, combining a two-position (three-way) valve to perform the Collect/Waste function and a multiposition valve to perform the Next vial function is usually necessary. Clarity Valve control modules also support the needed Next position command. The fraction collector can be easily created 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.

The Clarity software has several system files that are important for storing various data related to its functioning. The list of the files with default paths:

• C:\Clarity\Cfg\Clarity.cfg
  This file stores hardware configuration information, along with information about the last user who logged in to a specific instrument, and custom instrument pictures used in the Main window.
• C:\Clarity\Cfg\*.dsk
  This file stores information about the last used project (*.prj) and individual user preferences such as windows configuration and layout, tables and graph preferences, user columns, and more.
• C:\Clarity\DataFiles\Projects\*.prj
  This file stores information about project subdirectories (the project directory has the same name as the project *.prj file) and the last used method, sequence, SST method, chromatograms and other files.
• C:\Clarity\Cfg\Clarity.psw
  This file stores the list of users and their access rights.
• C:\Clarity\Cfg\Clarity.sno
  This file stores the identification of the station.

It is recommended to back up these files to prevent data loss in case of an accident. Please note that up to version 6.2, the Cfg subfolder did not exist, and the files were present in the root folder.

The sample rate needs to be set to provide enough points to describe the peaks of interest adequately. It is recommended that at least 30 points be reached per the narrowest peak width. The default value for DataApex's A/D converters is 10 Hz. This is suitable for most HPLC and packed column GC applications. The capillary GC and CE applications may need higher sample rates.

Accordingly, the Global Peak Width parameter must also be amended to match the sampling rate.

If you have bought an extension or control module license, you will get a new user code for the latest SW version and have to use the version compatible with the user code (if you have it, there is no need for reinstalling).

On top of that in the case of a new control module, reinstallation depends on how you installed Clarity originally (typical, full, or custom installation). If you miss any control module in the System Configuration window, you must reinstall Clarity.

An upgrade to the new major Clarity version (change in the first number before the dot) is paid and requires a new user code. Please refer to your price list under p/n C500 (C400/C591). All minor version updates (change in any number after the first dot) are provided free of charge and do not require a new user code. 

For more details, please refer to Clarity Upgrade Policy.

The installer of the current release version can be downloaded directly from the station, or from our websites.

We can offer Clarity (Lite) with analog data acquisition for each chromatograph and A/D converter Colibrick. Chromatographs/detectors need a standard analog output and means for local control, e.g., the instrument's keyboard. As a part of this basic solution, we also offer elementary synchronization with any autosampler.

Clarity Offline is a special version for data processing only where no real device is connected. It is to be installed on a different PC than a version for data acquisition. S/N for the offline version always starts with 98-xxxxx.

Only one Clarity software can be run on one PC.

A Clarity Control Module is an optional software module that enables autosampler, GC, GC-MS, HPLC/CE, or HPLC-MS control. Clarity can control chromatographic hardware listed in the datasheet List of currently controlled instruments (D004). Detailed descriptions of control options can be found on our website or in the corresponding control manuals.

Clarity Extension is an optional software extension that brings additional capabilities to Clarity. The information about available extensions, including technical documentation, can be found on our website.

We currently offer extensions for Photo Diode Array (PDA), Mass Spectroscopy (MS), Gel Permeation Chromatography (GPC), Natural Gas Analysis (NGA), Detailed Hydrocarbon Analysis (DHA), Capillary Electrophoresis (CE), Elemental Analysis (EA), and System Suitability Test (SST).

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