--- title: "How to Manage Monomer Aliases" slug: "how-to-manage-monomer-aliases" status: "new" updated: 2026-11-03T16:07:59Z published: 2026-11-03T16:07:59Z canonical: "docs.discngine.com/how-to-manage-monomer-aliases" --- > ## 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 Manage Monomer Aliases This guide shows how to give a monomer another name that HELM sequences can use, how to remove one, and how to add many at once. It uses sarcosine as the example: the public monomer `meG`, which a peptide library imported from elsewhere calls `Sar`. **Prerequisites**: the **Manager** or **Administrator** role in Biotoolkit Monomers. With the Viewer role you see the aliases but cannot change them. What an alias is, and the rules a name must follow, are explained in [Monomer Aliases](/public/docs/monomer-aliases). ## Add an alias from the monomer Use this when you are already looking at the monomer. 1. On the **Monomers** page, find the monomer, for example by typing `meG` in the search box, and click its symbol, or the pencil icon in the **Actions** column. The **Monomer management** dialog opens. The tag icon of the same column opens the shorter **Add an alias** dialog instead. 2. In the **Aliases** field, next to **Symbol**, type the new name: `Sar`. The line under the field says, as you type, whether the name is free: *"Sar" is free for this polymer type.* If the name is taken, the line names the monomer that has it, and the name cannot be added. 3. Press **Enter**, type `/`, or click **+** at the right end of the field. The name becomes a chip under the field and is saved at once: there is nothing else to click, and **Save changes** is not needed for it. Several names can be typed in one go, separated by `/`, for example `Sar/MeGly`. Public monomers accept aliases too. The alias belongs to your organisation, and the public monomer itself does not change. Public aliases are shown with a lock and cannot be removed. ### On a monomer you are creating The **Aliases** field works the same way in the form of a new monomer, but nothing is written before the monomer exists. Each name is shown as a chip marked *new*, and the line under the field reads *"Sar" will be added when you click Create.* The names are saved right after the monomer is created. If one of them is refused at that point, the monomer is still created, and the message that follows names the alias and the reason. ## Add an alias from the Aliases page Use this to name monomers without opening each one. 1. Open **Aliases** from the navigation menu. The page lists your organisation's aliases first, then the public ones, with the monomer each one names, its polymer type and its **Scope**: *Your organization* or *Public*. 2. Click **Add alias**. The **Add an alias** dialog opens. 3. In **Monomer**, search for and select the monomer, for example `meG`. 4. In **New alias**, type the name, or several separated by `/`. The line under the field says whether each name is free. 5. Click **Add**. The dialog closes, the list refreshes, and a message confirms what was added: *Added to meG: Sar.* If some names were refused, the dialog stays open with the reason for each of them, and the names that were free are added. ## Remove an alias Only your organisation's aliases can be removed. Either: - in the monomer dialog, click the cross on the alias chip; or - on the **Aliases** page, click **Remove** on the alias row and confirm *Remove the alias "Sar"? Your organization will no longer be able to use it for this monomer.* A sequence that uses the removed name no longer validates once the HELM services have refreshed, within five minutes. ## Add aliases in bulk The import page adds aliases from an optional `ALIASES` column, with the names separated by `/` in one cell: ``` SYMBOL,NAME,SMILES,POLYMER_TYPE,MONOMER_TYPE,NATURAL_ANALOG,RGROUPS,ALIASES MeNle,N-methyl-norleucine,CCCC[C@H](N(C)[*:1])C([*:2])=O,PEPTIDE,Backbone,L,R1:H;R2:OH,NMeNle/N-Me-Nle ``` An import only ever adds aliases: a name the monomer already has is accepted, and a name missing from the file is not removed. To add aliases to monomers that already exist, import their rows again with the `ALIASES` cell filled in: a row whose symbol exists updates that monomer. See [How to Import Monomers in Bulk](/public/docs/how-to-import-monomers-in-bulk) and the `ALIASES` column in [Import File Format](/public/docs/monomer-import-file-format). ## Turn a duplicate symbol into an alias When a file uses its own symbol for a structure that is already registered, for example `Sar` for the structure of `meG`, the row is refused by default. To make that symbol an alias instead: 1. On the import page, switch on **Register a known structure as an alias**. 2. Import the file. Each such row adds its symbol, and the aliases in its `ALIASES` cell, to the monomer that already has the structure. No monomer is created, and the import summary lists the rows that became aliases. Check that list: a structure drawn without its stereochemistry can match a different monomer than you expect. See [Canonical SMILES and Duplicate Detection](/public/docs/canonical-smiles-and-duplicate-detection). ## Check the alias in a sequence The catalogue search finds the monomer by its new name straight away, and the **Aliases** column of the **Monomers** report lists it. HELM validation, in Ideation or in the structure editor, accepts the alias within **five minutes**, the time the HELM services keep each organisation's library in memory. After that, `PEPTIDE1{T.[Sar].C}$$$$V2.0` validates, and the name is kept as written in the HELM and KET produced. ## Troubleshooting | Message | Cause and fix | | --- | --- | | *"meG" is already the symbol of Sarcosine (N-Methyl-Glycine) in the public library.* (or *in your organization*) | The name is a monomer's symbol. Use that monomer, or choose another name. | | *"Sar" is already an alias of Sarcosine (N-Methyl-Glycine) (symbol meG) in your organization.* | Another monomer, or this one, already answers to that name. A name points to one monomer per polymer type. | | *"Sar/MeGly" cannot be an alias: "/" separates several names, so no alias can contain it.* | `/` is the separator. Type the names separated by `/` to add them one by one. | | *"sar" is free for this polymer type* although `Sar` exists | Names are case-sensitive. `sar` would be a new, separate name. | | *Adding or removing an alias needs the Monomer Manager role.* | You have the Viewer role. Ask an administrator of your organisation. | | A public alias has no cross or no **Remove** button | Public aliases are read-only. | | The alias is in the catalogue, but HELM validation says the monomer is unknown | The HELM services have not refreshed yet. Wait five minutes and validate again. | ## Related - [Monomer Aliases](/public/docs/monomer-aliases): scope, rules and precedence - [REST API](/public/docs/monomer-service-rest-api): managing aliases from your own integration