How to set the Sequence Options in Clarity SW

Introduction

The Clarity Chromatography Software provides advanced tools for managing chromatographic sequences. Correct configuration of sequence options is crucial, as it defines how the sequence table operates, how runs are executed, and how results are stored. This article provides a step-by-step guide to setting up sequence options, based on an instructional video demonstration.

Accessing the Sequence Options Dialog

1. Open the Sequence Window.
2. Select the Options icon from the toolbar, or choose the Options item from the Sequence menu.
3. The Sequence Options dialog will appear, containing several configurable sections.

Sequence Description

At the top of the dialog, you will find a Description field. This is a free-text area where you can enter notes or identifiers for the sequence. Although optional, it is useful for documenting specific experiment details.

Sequence Mode

This section controls how Clarity handles the start of a sequence:

• Passive Mode
  • Clarity waits for an external start signal (e.g., from a connected device).
  • Commonly used for manual injections or with uncontrolled autosamplers.
  • The run begins when triggered by an external event, such as turning a manual injection valve.
• Active Mode (default option)
  • Clarity manages the entire process.
  • It waits for all devices to be ready, then signals the autosampler to inject.
  • Once injection is complete, the run starts automatically.
  • Suitable for the majority of automated workflows.

For more detailed instrument-specific settings, refer to Chapter 6 of the Getting Started Manual.

Idle Time in Active Mode

You can configure a delay (idle time) between the end of one run and the start of the next injection.
This feature is useful if:

• Devices require additional stabilization time.
• Too many commands at once could cause communication issues.

Sequence Row Selection

This field allows you to specify which rows in the sequence table will be executed.

• The software automatically sets the corresponding checkboxes in the Run column.
• You may still manually adjust them afterwards.

Counter Variable Settings

The counter variable can be configured here to increment automatically during the sequence.

• The counter can be used for labeling runs or files.
• It increments with every new run in the sequence.
• Depending on configuration, it may or may not reset.

File Name Conflict Resolution

When multiple analyses are initiated from one row, file naming conflicts may occur. Two options are available:

• Automatic (default)
  • Clarity appends a vial or injection variable to the file name, preventing duplication.
• Manual
  • The user resolves conflicts manually before saving.

Calibration and Sequence Usage

This section allows you to define the type of calibration cloning used within the sequence.

• For a full explanation of calibration settings, refer to the Calibration playlist provided by Clarity.

After Sequence Is Finished

At the end of the sequence, you can set a shutdown method for devices.

• For example, powering down pumps or turning off detectors.
• A detailed explanation is available in the related tutorial: “How to Shut Down Devices After the Sequence Is Finished.”

Saving and Applying Settings

Once configuration is complete:

1. Click OK to save the sequence options.
2. The parameters will apply immediately to the open sequence file.

Example Configuration (from video demonstration)

• Mode: Active
• Idle Time: 5 minutes
• Rows Executed: Only rows 2 and 4
• Row 4: End vial edited to allow multiple measurements
• File Name Conflicts: Solved automatically by appending the vial variable
• Counter Variable: Starts at 5, increments with each run, never resets

Conclusion

Configuring sequence options in Clarity Chromatography Software ensures smooth operation, consistent data handling, and efficient automation. By mastering the settings for sequence mode, idle time, file naming, calibration, and shutdown methods, analysts can tailor workflows to specific laboratory requirements.

For further guidance, users are encouraged to consult:

• Chapter 6 of the Getting Started Manual
• Calibration tutorials
• Device shutdown video guide