---
title: "How to Resolve Missing Monomers"
slug: "how-to-resolve-missing-monomers"
status: "update"
updated: 2026-10-14T09:22:11Z
published: 2026-10-14T09:22:11Z
canonical: "docs.discngine.com/how-to-resolve-missing-monomers"
---

> ## Documentation Index
> Fetch the complete documentation index at: https://docs.discngine.com/llms.txt
> Use this file to discover all available pages before exploring further.

# How to Resolve Missing Monomers

When a peptide references a monomer that Ideation cannot resolve, that peptide is imported with its HELM sequence preserved but **without** a full structure or calculated properties, and the dataset is flagged. This guide shows how to see what is missing, export the list, register the missing monomers, and sync the dataset — either the peptides that were blocked, or every peptide once a monomer's definition changed.

## Step 1: Spot the import issues

Wherever a dataset with import issues appears, an **amber warning triangle** appears with it. Hover it to read what happened — *"N structures imported with missing data"*, for example; click it to open the details.

![A peptide dataset page with the amber warning triangle in the title bar, a Missing Monomers column in the grid, and the affected rows highlighted](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/dataset-missing-monomers.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A02%3A42Z&se=2026-10-27T13%3A02%3A42Z&sr=c&sp=r&sig=Zq6zNHo7hPqHid9xIfFkNe%2FQEpqCNSbID4E3uX14tQU%3D)

You will find the same warning in several places, all opening the same dialog:

- the **dataset page** title bar;
- the **SAR report** title bar;
- the dataset **settings drawer**, on the **Details** tab next to the **Structures** count;
- **dataset cards** on the Home and project pages.

In the import wizard and on the import status page it appears instead as a banner stating what happened — *"N structures imported with missing data."*, *"N structures could not be imported."* or, for a mix, a breakdown such as *"22 import issues: 19 imported with missing data, 3 monomers not registered."* — with a **View Details** link.

In the grid, affected rows are **highlighted** and a **Missing Monomers** column lists the unresolved symbol(s). Those rows keep their HELM and their monomer drawing but show `0` atoms and no computed properties. The column only exists while something is unresolved — it disappears once everything resolves.

## Step 2: Read the reasons

The dialog's title states what happened, and its entries are grouped by what it means for your data:

- **Peptides not imported** — structures that are not in the dataset at all, such as a record the file parser could not read.
- **Peptides imported with missing data** — structures that are in the dataset and usable, with some of their data missing. Each entry says what: *chem chains, branches and bridges* when no structure detail could be built, *molecular weight, atom count, canonical SMILES and InChIKey* when no V2000 could be produced, *CTAB v3000*, or *monomer count*. A peptide with a missing monomer is listed here: it keeps its backbone sequence and gets the rest once the monomer is registered and the dataset synced.
- **Monomers not registered** — rows of your monomer library file that could not be read, or that the Monomer Service refused, with the reason (see below).
- **Reported at import** — entries of datasets imported before this distinction was recorded; whether those structures are in the dataset is not known.

Each entry shows the primary identifier, the reason, and what is missing when that was recorded, under a **Missing data** line. A coloured **Severity** line says how much the entry matters for your SAR analysis:

- In orange, a **warning**: the peptide is imported and usable, but some of its data is missing, such as *molecular weight, atom count, canonical SMILES and InChIKey*, *CTAB v3000* or *monomer count*. It can still be fully used in SAR analysis.
- In red, an **error**: the peptide is not imported at all, or it is imported with *chem chains, branches and bridges* missing, so only its backbone is available in SAR slides. Fix these first.

Monomer library rows have no severity (the peptides that use them are listed as errors), and neither do entries from datasets imported before this detail was recorded.

When you attached a monomer library file, rows of that file Ideation could not read are listed here too, as *Monomer "X" (library row N)*, with the reason the row was unreadable — and so are rows the Monomer Service refused to register, as *Monomer "X" (library)*, with the service's reason: invalid chemistry, a structure already registered under another symbol, a template that could not be built. Both appear only when a peptide of the dataset uses that monomer. The peptides built from it appear in the same list as missing it, so the library row is the explanation of those peptide entries. See [How to Create a Peptide Dataset](/public/docs/how-to-create-peptide-dataset).

**Export CSV**, at the top of the list, downloads the whole list as `structure-issues.csv` with one row per entry: the **source** file (`dataset` or `monomer library`), the **identifier** (peptide ID or monomer symbol), the **outcome** (`not imported`, `imported with missing data`, `not registered` for a library row, `not recorded` for an entry from before outcomes were tracked), the **severity** (`error` or `warning`, empty for library rows and legacy records), the **missing data**, the **structure** as written in your file (the peptide's HELM or the monomer's SMILES) and the **error**. It is the quickest way to fix a large file at the source and re-import it.

Entries written before this release carry no structure, so their **structure** cell is empty until the dataset is re-imported or synced.

![The import issues dialog: structures grouped by outcome with per-structure reasons and missing data, and a footer box listing the missing monomers with a Biotoolkit Monomer Service App link and a Sync Monomers button](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/skipped-structures-dialog.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A02%3A42Z&se=2026-10-27T13%3A02%3A42Z&sr=c&sp=r&sig=Zq6zNHo7hPqHid9xIfFkNe%2FQEpqCNSbID4E3uX14tQU%3D)

Not every entry is a missing-monomer case, and the distinction decides what you can do about it.

**Missing-monomer reasons** always take the same shape:

> HELM sequence preserved. Missing monomers: `Zzz1` (not found in Biotoolkit Monomer Service). Register missing monomers in the Biotoolkit Monomer Service, then sync this dataset to get the full structure and calculated properties.

The symbols are grouped by cause, and the cause in parentheses tells you *why* that particular symbol did not resolve:

| Cause | Meaning |
| --- | --- |
| `not found in Biotoolkit Monomer Service` | The symbol is unknown and no structure was available to register it. **Register it** (Step 3). |
| `conflicts with existing public/private symbol "X"` | The structure is already registered under another symbol, in a way Ideation could not adopt automatically. |
| `invalid chemistry: …` | The Biotoolkit Monomer Service rejected the structure supplied for the symbol. |
| `invalid template: …` | The monomer template was malformed — for example its R-group labels don't match. |
| `invalid symbol format` | The symbol itself is not a shape the service accepts. |
| `template conversion failed` | The supplied structure could not be converted into a monomer template. |
| `Biotoolkit Monomer Service unavailable` | A transient service problem for that symbol. Sync again later. |

**Structural / HELM reasons** are problems in the peptide itself and registering a monomer will *not* fix them — the HELM has to be corrected at the source and the dataset re-imported. [HELM Rules for Peptide Import](/public/docs/reference-helm-rules) lists the rules a HELM must follow. For example:

- *"PEPTIDE1,CHEM1,30:R3-1:R1 is not valid: Attachment point R3 for monomer source `Dap_Ac` doesn't exists"*
- *"HELM conversion failed: Unknown attachment point 'R2' in monomer …"*
- *"No KET representation could be produced from V3000 or HELM"*

One reason per peptide

A peptide is never reported twice. If it is listed because of a missing monomer, Ideation does not also report a generic conversion failure for it.

Duplication check on structure

The Biotoolkit Monomer Service runs a **duplication check on structure**, so a monomer may already be registered under a **different symbol**. In that case Ideation matches your symbol to the existing entry instead of registering a duplicate — which is why a symbol can resolve even though you never registered that exact name.

## Step 3: Register the missing monomers

If the Biotoolkit Monomer Service still reports monomers as missing, the dialog ends with a highlighted box naming them:

> The following monomers are missing from the Biotoolkit Monomer Service: **Zzz1**. Register them in the **Biotoolkit Monomer Service App**, then click "Sync Monomers" button to synchronize. It will recompute structures and properties.

Open the **Biotoolkit Monomer Service App** link — it points at the service for your environment — and register each listed monomer with its symbol and structure, then return to Ideation.

When the sync box appears

This box only appears while the service actually reports something missing. A dialog that lists only structural failures, or whose monomers have since been registered, shows no sync action. While Ideation is checking you will briefly see *"Checking for missing monomers…"*; if the check itself fails it says *"Could not check the Biotoolkit Monomer Service for missing monomers."*

Registration is permanent and organization-wide

Once a non-natural monomer is in the Biotoolkit Monomer Service, every current and future dataset that uses the same symbol resolves it automatically — you never need to register it again. Registration only **adds** new monomers; existing ones are never overwritten.

## Step 4: Sync the dataset

There are two ways to sync, and they do not recompute the same peptides.

**From the dialog — the blocked peptides only.** Back in the dialog, click **Sync monomers**. Ideation re-resolves the dataset's still-missing monomers against the service and, for any that are now available, recomputes the structure and properties of the peptides that were blocked. Peptides that imported fine are not touched. When no monomer is missing but some peptides were imported with data missing (even only a monomer count), the dialog offers the full sync below instead: a conversion can fail because of how a monomer is defined (its structure, stereo or cap groups), and once you correct that monomer, only a full sync rebuilds those peptides.

**From the dataset title bar — every peptide.** The **Sync monomers** icon (the circular arrows, right of the import issues warning) is available on every peptide dataset you can edit, whether or not anything was reported. It rebuilds **all** the dataset's peptides from their HELM: monomers are resolved again, structures (KET, V3000, V2000, SMILES) are converted again, and molecular weight and atom count are recomputed. Use it after a monomer was **corrected** on the Biotoolkit Monomer Service — its cap groups, its structure — since such a change alters the chemistry of peptides that had imported without a problem. A confirmation dialog states what will happen before anything starts; the icon is disabled while the dataset is being processed.

![The dataset title bar actions: the role chip, the Ready status, the import issues warning, the Sync monomers icon, share, users and settings](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/dataset-title-bar-sync-monomers.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A02%3A42Z&se=2026-10-27T13%3A02%3A42Z&sr=c&sp=r&sig=Zq6zNHo7hPqHid9xIfFkNe%2FQEpqCNSbID4E3uX14tQU%3D)

![The Sync monomers for all peptides confirmation dialog explaining that every peptide is rebuilt from its HELM and that the dataset is unavailable while the sync runs](https://cdn.document360.io/dde9293e-c107-4b3e-9774-9c9c296ed970/Images/Documentation/sync-monomers-confirm-dialog.png?sv=2026-02-06&spr=https&st=2026-10-27T12%3A02%3A42Z&se=2026-10-27T13%3A02%3A42Z&sr=c&sp=r&sig=Zq6zNHo7hPqHid9xIfFkNe%2FQEpqCNSbID4E3uX14tQU%3D)

Peptides that could not be converted are retried as well, and the issue list is refreshed the same way as below — including peptides that fail for the first time, which join it.

You will get one of three responses:

| Message | Meaning |
| --- | --- |
| **Monomer synchronization started.** | The background job is running. |
| **The dataset is not ready to synchronize. Please try again shortly.** | The dataset is busy — for example a sync is already running. Nothing was started; retry in a moment. |
| **Error syncing monomers. …** | The request itself failed. |

The sync runs in the background. On a dataset large enough for it to take a while, the dialog follows along: its title changes to **Synchronizing Monomers**, the issue list is replaced by a live progress timeline — **Initializing → Synchronizing Monomers → Parsing Peptide Sequences → Ready** — with an *"N / M structures recomputed"* progress bar. You can close the dialog at any time; the work continues.

When it finishes:

- peptides that now resolve are **removed** from the issue list, so the warning count drops (and the warning disappears entirely once the list is empty);
- a *Monomer "X" (library row N)* entry is **removed** too once the Biotoolkit Monomer Service knows that monomer, since the peptides it explained now convert;
- peptides still missing a monomer keep a **refreshed** reason, so the causes you read are always current;
- peptides that fail for a structural reason keep their entry, with a refreshed reason when they were recomputed;
- after a full sync, a peptide that fails for the first time is **added** to the list, with its HELM.

Manual sync only

Syncing is always user-initiated — Ideation never auto-syncs.

If the Biotoolkit Monomer Service is unreachable

The sync ends without changing anything and the dataset returns to **Ready**; you are not notified separately. The unreachability shows up as `Biotoolkit Monomer Service unavailable` in the per-peptide reasons, or as *"Could not check the Biotoolkit Monomer Service for missing monomers."* in the dialog. Retry once the service is back.

## Next steps

- [How to Create a Peptide SAR Report](/public/docs/how-to-create-peptide-sar-report)
- [Understanding Peptides in Ideation](/public/docs/explanation-understanding-peptides)