Migrate from ISIS for Excel to JChem for Excel: Step-by-Step Converter Tutorial

ISIS for Excel to JChem for Excel Converter: Quick Guide and Best Practices

What it is

ISIS for Excel and JChem for Excel are Excel add-ins used by chemists to store, view, and manipulate chemical structures and associated data directly in spreadsheets. A converter migrates spreadsheets and embedded chemical objects from ISIS for Excel format to JChem for Excel format, preserving structures, identifiers, and column mappings.

Pre-conversion checklist

• Backup: Save original files and a copy of the working directory.
• Software versions: Ensure compatible versions of Excel, ISIS for Excel (legacy), JChem for Excel, and the converter tool.
• Dependencies: Confirm required .NET frameworks, Java (if JChem needs it), and any licensing for JChem tools.
• Test set: Create a representative sample workbook (structures, InChI/SMILES, images, metadata, custom columns).
• User permissions: Run with an account that can install add-ins and write files.

Step‑by‑step conversion (typical workflow)

1. Install JChem for Excel and the converter tool per vendor instructions.
2. Close Excel, then register/enable both add-ins.
3. Open the sample workbook in Excel.
4. Run the converter (menu or command-line option). Choose:
   • Input workbook(s)
   • Output location (new file or overwrite)
   • Conversion options (preserve original columns, map structure columns, convert images to embedded structures)
5. Verify mapping: confirm which ISIS columns map to JChem structure fields (e.g., ISIS structure object → JChem structure cell; SMILES/InChI columns → structure generation).
6. Run conversion on sample.
7. Inspect converted workbook:
   • Open structure inspector in JChem for Excel to confirm molecules render correctly.
   • Check identifiers and calculated properties (mol weight, formula).
   • Validate searchable indexes if used.
8. If acceptable, run batch conversion on full dataset.
9. Archive originals and record conversion log.

Best practices

• Map columns explicitly: Define and document how each ISIS field maps to JChem fields to avoid data loss.
• Preserve originals: Never overwrite originals until validation completes.
• Validate chemically: Use automated checks (SMILES↔structure round-trip, InChI matching) on a sample subset.
• Handle images carefully: Convert embedded images to molecule objects where possible; otherwise keep originals in a backup.
• Manage large files: Split very large workbooks to avoid Excel performance limits; consider command-line batch conversion if supported.
• Track provenance: Add a conversion metadata sheet with tool version, date (Feb 5, 2026), and operator name.
• Automate and log: Use scripting or command-line options to automate repetitive conversions and retain logs for audit.
• Licensing & support: Ensure valid JChem licenses; contact vendor support for edge-case structures or proprietary fields.

Troubleshooting common issues

• Molecules fail to render: check for missing structure columns (SMILES/InChI) and ensure JChem can parse them.
• Loss of custom metadata: verify converter supports custom column types; export metadata separately if not.
• Performance slow: reduce workbook size, disable Excel auto-calculation, or use batch CLI tools.
• Differences in computed properties: re-run property calculations in JChem after conversion to ensure consistency.

Quick validation checklist

• Structures render in JChem for Excel.
• SMILES/InChI/InChIKey values match originals (spot-check 10–20 entries).
• Calculated molecular properties match expectations.
• Custom columns present and correctly mapped.
• Conversion log saved and originals archived.

If you want, I can draft a ready-to-run checklist sheet you can paste into Excel or provide a sample conversion log template.