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.

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.

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.

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 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.

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:

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. 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"

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.

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.

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.

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:

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.

Next steps

• How to Create a Peptide SAR Report
• Understanding Peptides in Ideation