Tips & Best Practices

Here's what we've learned works best for SmartAdd. These tips will save you time and headaches.

Before You Start

Name Your Files Well

Here's the thing: you'll be building the folder structure manually in SmartAdd, so clear file names are your best friend.

What makes a good file name?

Include the sample or compound identifier
Specify the analysis type
Add relevant parameters (like solvent or frequency)
Be consistent with your naming style

File Naming Conventions

Type	Good Example	Bad Example
NMR	`compound_A_1H_NMR_400MHz_CDCl3.jdx`	`data.jdx`
MS	`sample_001_ESI_MS_positive.mzML`	`new_file_final_v3.mzML`
IR	`product_IR_KBr.jdx`	`spectrum@#$.jdx`
Metadata	`synthesis_notes_2024-01-15.txt`	`notes.txt`

Things to avoid:

❌ Special characters like @, #, $, %, &
❌ Spaces (use underscores or hyphens)
❌ Generic names like data, file, new
❌ Version numbers unless you really need them (_v1, _v2, _final)

Gather Everything First

Before you upload, collect all the files you'll need:

📊 All your spectra (NMR, MS, IR, etc.)
🧬 Structure files (MOL format, text)
📝 Instrument logs
📋 Metadata with experimental conditions
📄 Any notes (synthesis procedures, observations)

Upload Strategy

Whether you upload a ZIP or individual files, SmartAdd puts everything in an input list. Then you manually drag files to assign them to samples and analyses.

While Using SmartAdd

Work One Sample at a Time

Trust us on this - complete each sample fully before starting the next one:

Click "Add Sample"
Fill in the properties (name, SMILES, amount, etc.)
Drag files from the input list to this sample
Add analyses and attach the analytical files
Done? Move to the next sample

Why this works better:

Fewer mistakes
You can track your progress easily
Less overwhelming when you have lots of data
You won't forget to assign files

Don't Forget!

Drag files from the left panel (input list) to the right panel (assignment tree). If you don't assign a file, it won't be in your export!

Keep Names Consistent

Pick a naming style and stick with it throughout your project:

Samples: COMP_001, COMP_002, COMP_003
Reactions: RXN_Suzuki_001, RXN_Grignard_002
Analyses: NMR_1H_001, MS_ESI_001

Check Your SMILES

SmartAdd validates SMILES in real-time:

Type in your molecular structure using SMILES notation
Look for the green indicator (valid) or red (invalid)
Fix any errors before moving on
Not sure about your SMILES? Use ketcherDemo to generate a valid molfile

Group Samples into Reactions

When you have a reaction with multiple samples:

Add all relevant samples to the reaction
Assign roles (reactant, product, solvent)
SmartAdd will automatically sort them by role
Set the reaction scheme type for better visualization

Always Include Units

Numbers without units are meaningless. Always add them:

Field	❌ Without Units	✅ With Units
Amount	`100`	`100 mg`
Volume	`5`	`5 mL`
Time	`24`	`24 h`
Temperature	`25`	`25 °C`

Write Good Descriptions

Future you will thank present you for being descriptive:

Samples:

❌ "Sample A"
✅ "Suzuki coupling product, white solid, synthesized 2024-01-15"

Reactions:

❌ "Reaction 1"
✅ "Pd-catalyzed Suzuki coupling, RT, 24h, N₂ atmosphere, THF solvent"

Analyses:

❌ "NMR data"
✅ "¹H NMR (400 MHz, CDCl₃)"

Master the Two-Panel Layout

Left Panel (Input List):

This is where all your uploaded files live
Drag files from here to assign them to samples

Right Panel (Assignment Tree):

This is your workspace with samples and reactions
Drag files here to attach them
Click on any item to edit its properties

Pro tip: Expand the section you're working on, and collapse the ones you've finished. Keeps things tidy!

How to Organize Your Tree

A well-organized tree looks like this:

✅ Good:
📦 Assignment Tree
  ├─ 🧪 Reaction: Suzuki Coupling
  │   ├─ 📋 Sample: Reactant A (role: reactant)
  │   │   └─ 📊 Analyses
  │   │       └─ 📊 1H NMR
  │   └─ 📋 Sample: Product B (role: product)
  │       └─ 📊 Analyses
  │           ├─ 📊 1H NMR
  │           └─ 📊 13C NMR
  └─ 📋 Sample: Standalone Sample
      └─ 📊 Analyses

❌ Avoid:
📦 Assignment Tree
  ├─ 📋 Sample (vague name)
  ├─ 📋 Sample (no files attached)
  └─ 🧪 Reaction (empty)

Before You Export

Quick Checklist

Before you click "Download as ZIP", run through this:

Samples:

Reactions:

Analyses:

Common Mistakes

Watch out for these - they're easy to make:

Mistake	The Problem	The Fix
Invalid SMILES	Wrong structures	Check for the green validation indicator
Missing units	Data becomes meaningless	Always include units with numbers
Generic names	Can't tell items apart	Use descriptive, unique names
Unassigned roles	Unclear what's what in reactions	Assign roles to all samples
Files not assigned	They won't be in your export	Drag all files to the tree
Empty tree	Nothing to export	Use "Add Sample" and "Add Reaction"
No filtering	Unwanted data in export	Use inclusion/exclusion controls
No descriptions	Lost context later	Add brief descriptions
Skipping validation	Errors when uploading	Review everything first

Advanced Tips

Keep track of versions:

Name files with dates for checkpoints
Include your initials in filenames
Keep a simple changelog
Back up your ZIPs to shared storage

Before You Start​

Name Your Files Well​

File Naming Conventions​

Gather Everything First​

While Using SmartAdd​

Work One Sample at a Time​

Keep Names Consistent​

Check Your SMILES​

Group Samples into Reactions​

Always Include Units​

Write Good Descriptions​

Master the Two-Panel Layout​

How to Organize Your Tree​

Before You Export​

Quick Checklist​

Common Mistakes​

Advanced Tips​