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
On the dataset page, a warning in the title bar (warning sign icon) reads "N structures skipped during import" — this is the entry point for resolving them. In the grid, a Missing Monomers column flags the unresolved symbol(s) on affected rows (those rows show 0 monomers and no computed structure).
Step 2: Review what was skipped, and resolve it from the dialog
Click the N structures skipped during import warning to open the "N Structures Could Not Be Imported" dialog. It lists each skipped structure with its reason, and — at the bottom — a highlighted box that summarizes the monomers missing from the Monomer Service and gives you the tools to fix them: a Monomer Service App link and a Sync Monomers button.
Not every skipped structure is a missing-monomer case. Reasons fall into two groups:
- Missing monomer — for example "The following monomers are missing from the Monomer Service:
aMePhe_4F,Ala_cPent". These are fixed by registering the monomers (Steps 3–4). - Structural / HELM errors — for example "Attachment point R3 for monomer source
Dap_Acdoesn't exist" or "HELM conversion failed: Unknown attachment point 'R2' in monomer …". These are problems in the peptide's HELM itself, and registering a monomer will not fix them — the HELM needs correcting at the source.
The Monomer Service runs a duplication check on structure, so a monomer may already be registered under a different symbol (an alias). In that case Ideation matches your symbol to the existing entry instead of registering a duplicate — so a symbol can resolve even though you never registered that exact name.
Step 3: Register the missing monomers
From the dialog's footer box, open the Monomer Service App — the link points at your environment's service; the production app is at https://monomer.discngine.cloud/ords/f?p=prod_t1_dng_monomer. Register each listed monomer (its symbol and structure) there, then return to Ideation.
Registering a monomer is permanent and organization-wide. Once a non-natural monomer is in the 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 in the background. Peptides whose monomers are still missing (or that failed for a structural reason) are left untouched.
Syncing is always user-initiated — Ideation never auto-syncs. The recompute runs as a background job; the dataset returns to Ready when it finishes.
If the Monomer Service is unreachable, the sync fails with a "service unavailable" message. Retry once the service is back.