Troubleshooting Guide

Having trouble? Don't worry - most issues have simple solutions. Here are the most common problems and how to fix them.

Upload Problems

My ZIP file won't upload

Try these fixes:

• Make sure your file isn't too large - try splitting it into smaller ZIPs
• Refresh your browser (Ctrl+F5 or Cmd+Shift+R)
• Try a different browser (Chrome or Firefox work best)
• Check your internet connection

If the ZIP file seems corrupted, just recreate it and try again.

I uploaded files but can't find them

For Regular File Uploads: SmartAdd doesn't automatically organize your analytical files. After uploading:

1. Look in the input list on the left - your files are there
2. Create samples and reactions using the buttons in the right panel
3. Drag analytical files from the left input list to samples/analyses in the right tree

warning

Files that stay in the input list won't be exported! Make sure to drag everything you need to the assignment tree.

For Chemscanner ZIP and Excel Templates: These work differently - they auto-generate the collection structure:

• Chemscanner ZIPs (with export.json) create samples and reactions automatically
• Excel templates generate the complete collection hierarchy from your spreadsheet
• The generated structure appears in the assignment tree (right panel)
• After import, drag your analytical files from the input list to the generated structure
• You can edit and refine the auto-generated structure as needed

Chemscanner ZIP not auto-generating structure

If your Chemscanner ZIP uploads but doesn't create samples/reactions:

• Make sure it's a valid Chemscanner export containing export.json (not a regular ZIP)
• Check the ZIP file isn't corrupted
• Look for error messages in the upload area
• Try extracting the ZIP manually to verify export.json exists
• Check browser console for processing errors

Workaround: If auto-processing fails, you can still work manually:

1. Any analytical files from the ZIP will appear in the input list
2. Manually create samples and reactions using the buttons
3. Drag the files from input list to your manually-created structure

Excel template not auto-generating structure

If your Excel file uploads but doesn't create samples/reactions:

• Using the official template? You must use the SmartAdd Excel template provided by the SmartAdd
• Check file format: Must be .xlsx (not .xls or .csv)
• Check file size: Very large files may take time to process
• Check template structure:
  • Must follow the official template format exactly
  • Column headers must not be modified
  • SMILES notation should be valid
  • Required fields should be filled
• Look for error messages: They indicate what went wrong

Common Excel Template Issues:

• Not using the official template - custom Excel files won't work
• Modified or missing required column headers
• Invalid SMILES notation in cells
• Merged cells or complex formatting
• Empty rows breaking the data sequence
• Extra columns or sheets not in the template

Fix:

1. Get the official template from the import structure modal
2. Don't modify the template structure or column headers
3. Use plain text formatting (no merged cells, no fancy formatting)
4. Validate SMILES before uploading (use ChemDraw or similar)
5. Remove empty rows and extra columns
6. Fill all required fields

Workaround: If auto-processing fails:

1. Manually create samples and reactions using the buttons
2. Copy data from Excel and paste into SmartAdd properties
3. Or request a working example template from the Chemotion team

Editing Problems

I can't edit anything

Make sure you're clicking on an actual item (like a sample or reaction), not a folder. The properties panel should appear on the right when you select something.

If fields still look grayed out, try refreshing your browser or updating to the latest version.

My changes disappear when switching items

This is fixed in the latest version! If you're still experiencing this:

• Make sure you're using the current version of SmartAdd
• Wait for the debounce delay (1 second for rich text, 0.5 seconds for regular fields)
• Press Tab or click outside the field to trigger an immediate save
• Check your browser console for any errors

Rich text editor isn't loading

The Quill editor loads dynamically. If you see a gray loading box that never loads:

• Refresh your browser (Ctrl+F5 or Cmd+Shift+R)
• Clear your browser cache
• Check if JavaScript is enabled
• Try a different browser (Chrome or Firefox work best)
• Check browser console for loading errors

Ketcher modal won't open

If the "Draw Structure" button doesn't work:

• Make sure pop-ups aren't blocked for this site
• Check if you clicked the right button (should be next to "Upload File")
• Try refreshing the page
• Clear your browser cache
• Check browser console for errors

Ketcher shows blank screen

If the Ketcher editor opens but shows nothing:

• Wait a few seconds - it may still be loading
• Check your internet connection (Ketcher loads from CDN)
• Try closing and reopening the modal
• Refresh the entire page and try again

SMILES validation shows errors

The easiest fix: use a molecular structure editor like Ketcher or ChemDraw to generate valid SMILES, then copy and paste into SmartAdd.

Or use SmartAdd's built-in Ketcher:

1. Click "Draw Structure" in the MOL file field
2. Draw your molecule in Ketcher
3. Save to generate a MOL file
4. Use Ketcher's export function to generate SMILES if needed

Common SMILES mistakes to avoid:

• Mismatched brackets or parentheses
• Typos in atom symbols
• Unclosed rings

MOL file validation fails

If your uploaded MOL file shows validation errors:

• Check the error message: It tells you exactly what's wrong
• Common issues:
  • File too short (needs at least 4 lines)
  • Invalid atom count
  • Invalid bond count
  • Malformed atom or bond lines
• Fix: Use the "Draw Structure" button to create a valid MOL file
• Alternative: Use ChemDraw or another tool to generate a proper MOL file

Formatting disappears from descriptions

If your rich text formatting isn't saved:

• The Quill editor has a 1-second debounce delay
• Wait a moment after formatting before switching items
• Click outside the editor to trigger immediate save
• Check that you're not in read-only mode

Export Issues

Download button doesn't work

First, check if your browser is blocking the download:

• Look for a notification about blocked pop-ups
• Check your browser's download settings
• Try disabling ad blockers temporarily
• Use incognito/private mode

My export is missing data

This is the most common issue!

Before exporting, check:

• Did you drag all files from the input list (left) to the assignment tree (right)?
• Are all your samples and reactions created?
• Expand the tree nodes - can you see all your files attached?

Remember: Only files in the assignment tree get exported!

Direct upload to Chemotion isn't working

Connection problems:

• Double-check the server URL (should start with https://)
• Make sure you're on the right network (VPN if needed)
• Test the URL in your browser first

Login issues:

• Usernames and passwords are case-sensitive
• Try logging into Chemotion directly to verify your credentials
• Contact your Chemotion administrator if you're sure the credentials are correct

Upload fails or times out:

• Your collection might be too large - try breaking it into smaller batches
• Check your network connection
• As a backup, use "Download as ZIP" and import manually

Performance Issues

SmartAdd is running slow

Quick fixes:

• Close other browser tabs
• Clear your browser cache
• Restart your browser
• For very large projects (100+ samples), work in smaller batches

Display looks weird

• Reset your browser zoom to 100% (Ctrl+0 or Cmd+0)
• Make sure your browser window is large enough
• Try refreshing the page

Still Stuck?

Quick fixes to try first:

1. Refresh the page
2. Clear your browser cache
3. Try a different browser
4. Check the video tutorial for visual guidance

Need more help?

When reaching out for support, it helps to include:

• What browser you're using
• What you were trying to do
• Any error messages you see (screenshots are great!)
• An example file if relevant

Quick Reference

Problem	Quick Fix
Upload stuck	Refresh page, try smaller files
Can't find uploaded files	Check input list (left) for analytical files
Chemscanner ZIP not auto-generating	Verify it has export.json, check console for errors
Excel template not auto-generating	Check .xlsx format, validate SMILES, simplify formatting
Export is empty	Drag files from input list to assignment tree
Can't edit fields	Click on an actual item, not a folder
Changes don't save	Press Enter or click outside field first
Changes disappear when switching	Wait for debounce delay, or press Tab
Rich text editor not loading	Refresh page, clear cache, check JavaScript
Ketcher won't open	Check pop-up blocker, refresh page
Ketcher blank screen	Wait for loading, check internet connection
Invalid SMILES	Use Ketcher or ChemDraw to generate valid SMILES
MOL file validation fails	Check error message, use "Draw Structure"
Formatting disappears	Wait 1 second after editing, click outside field
Download blocked	Check pop-up blocker settings
Can't login to Chemotion	Verify credentials are case-sensitive and correct
App running slow	Close browser tabs, clear cache

tip

Most problems can be solved with a simple refresh or by making sure files are dragged from the input list to the assignment tree!