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.

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 and the ALIASES column in 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.

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

Related

• Monomer Aliases: scope, rules and precedence
• REST API: managing aliases from your own integration