Signals Notebook: Importing or Inserting HELM with custom monomer(s) fails with an symbol interpretation error

Overview

This article explains how to resolve symbol interpretation errors when working with custom monomers in HELM notation within Signals Notebook. If you encounter errors when inserting or importing HELM data containing custom monomers, this guide will help you identify and fix the issue.

Problem

HELM notation requires multi-character symbols to be enclosed in square brackets ([]). If you omit the brackets, Signals Notebook cannot interpret the HELM string, resulting in an error during insertion or import operations.

Solution

Always enclose multi-character symbols for your custom monomers in square brackets when writing HELM notation.

Example

If you have a custom peptide monomer named MyAmino1, a correct HELM notation is:

Correct: PEPTIDE1{A.[MyAmino1].C}$$$$V2.0
Incorrect: PEPTIDE1{A.MyAmino1.C}$$$$V2.0

Typical Scenarios

Scenario 1: Inserting HELM in the HELM editor of the Chemical Drawing element

When you use the "Text" tab of HELM Editor to insert HELM data with custom monomers, you may see the following error.

The text could not be converted to a sequence

Scenario 2: Bulk importing compounds with chemical structure in HELM notation

When you bulk import compounds whose chemical structures are in HELM notation containing custom monomers, you may see the following error in the Material Bulk Report.

The specified HELM content is not understood or not supported.