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 was skipped, register the missing monomers, and sync the dataset.
Step 1: Spot the skipped structures
Wherever a dataset with skipped structures appears, an amber warning triangle appears with it. Hover it to read "N structures skipped during import"; 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 — "N structures were skipped during import." — with a View Failed Structures 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 is titled "N Structures Could Not Be Imported" and lists each skipped structure under its primary identifier with the reason it was skipped.
Not every skipped structure 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. For example:
- "PEPTIDE1,CHEM1,30:R3-1:R1 is not valid: Attachment point R3 for monomer source
Dap_Acdoesn't exists" - "HELM conversion failed: Unknown attachment point 'R2' in monomer …"
- "No KET representation could be produced from V3000 or HELM"
A peptide is never reported twice. If it was skipped because of a missing monomer, Ideation does not also report a generic conversion failure for it.
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.
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."
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
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 their structure and properties.
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 and only revisits the peptides that previously failed. On a dataset large enough for it to take a while, the dialog follows along: its title changes to Synchronizing Monomers, the skipped 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 skipped list, so the warning count drops (and the warning disappears entirely once the list is empty);
- peptides still missing a monomer keep a refreshed reason, so the causes you read are always current;
- peptides that fail for a structural reason are left untouched.
Syncing is always user-initiated — Ideation never auto-syncs.
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.