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How to find a ChemStation run on disk and open it

You ran a sequence in ChemStation and now need one run as a file: to copy it to another PC, send it to a colleague, or look at it without the instrument. This is where ChemStation keeps the data, how the folders are named, and how to open a run, with or without ChemStation.

Where ChemStation saves data

A lab can point ChemStation at another folder or drive. To see which one yours uses: View > Preferences, tab Paths, lists the data locations, and the Path box in the Sequence Parameters dialog shows where the current sequence writes. If your lab stores data on a central server (Agilent ECM), the runs may not be on the local disk at all: ask whoever looks after that server.

How a sequence is stored

With Unique Folder Creation on, every sequence gets its own folder inside the data path, created when the sequence starts. Its name follows the Name Pattern on the Sequence tab of View > Preferences, often the sequence name with the date and time. The folder holds:

With it off, the .D folders go straight into the folder set in Sequence Parameters, without method copies.

The .D folder names depend on the sequence settings:

Inside a .D folder are the signals (.CH files such as DAD1A.CH or FID1A.CH), DAD spectra (.UV), MS data (.MS) on GC-MS, the sample information (SAMPLE.MAC), the run log (RUN.LOG) and, if the report was saved to file, REPORT.TXT and REPORT.PDF.

Finding one run

Start in the data folder above. Sequence folders that carry the date in their name, or sorting by Date modified in File Explorer, get you to the right day. With automatic names, the vial number is in the folder name; search for 017-* to find all injections from vial 17. The sample name is not in an automatic folder name. Drop the sequence folder on Nagura Lab instead: it lists every run with its sample name, date, method and vial in one table.

Copying it off the instrument PC

Copy the whole .D folder, not a single .CH file: a run is a group of files. To keep a sequence loadable as one sequence in ChemStation, copy the whole sequence folder, including the .B batch file; without it, ChemStation treats the folder as separate runs (Agilent Community).

Opening it in ChemStation

  1. Use the offline copy of ChemStation: the online session's Data Analysis is not available while the instrument is acquiring.
  2. In the Data Analysis view, select the sequence folder in the ChemStation Explorer. The navigation table lists its runs; right-click a run to load, overlay, export or print it.
  3. For a single run, File > Load Signal. If your runs are in a folder ChemStation does not list, add it on the Paths tab of View > Preferences first.

Menu names differ between ChemStation revisions. Paths, folder layout and file names are from Agilent's manual Understanding Your Agilent ChemStation (G2070-91126, revision B.04) and Agilent Japan's backup notes for OpenLab CDS ChemStation Edition (PDF, Japanese).

Opening it without ChemStation

  1. Open Nagura Lab and drop the .D folder on the page, or the whole sequence folder: methods, sequence, batch file and logbook are skipped, and every run opens.
  2. Tick signals to overlay runs; click a DAD or MS trace to see the spectrum at that time.
  3. Download a chromatogram as CSV or PNG, or every run at once as a zip of CSV files.

The files are decoded on your computer and never uploaded. Nagura Lab shows the signals as recorded; it does not reproduce ChemStation's integration or report.

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