How to Create or Edit a Monomer

This guide shows how to register a single monomer from its SMILES, check the drawn structure, set its cap groups, and later correct it. It uses diethylglycine (Deg), an achiral dialkyl glycine used like Aib to stabilise helices, as the worked example, then an N-methylated norleucine whose cap group was left wrong to show what an edit looks like.

Prerequisites: the Manager or Administrator role in Biotoolkit Monomers. You need the monomer's structure as SMILES or CXSMILES, and you need to know where it attaches to its neighbours.

Public monomers are read-only

Only your organisation's private monomers can be created, edited or deleted. A public monomer can be opened to read its definition and structure, but nothing in it can be changed. See Public Monomers.

Step 1: Write the SMILES with numbered attachment points

An attachment point is written as [*:n], where n is the R-group number. For a peptide backbone monomer, the convention is:

R1 on the amine nitrogen (the N-terminal side),
R2 on the carbonyl carbon (the C-terminal side),
R3 on the side chain, if the monomer can branch.

Diethylglycine is glycine with two ethyl groups on the alpha carbon:

CCC(CC)(N[*:1])C([*:2])=O

The two [*:n] atoms stand for the bonds the monomer will make inside a chain, so the SMILES describes the residue, not the free amino acid. Write the structure with its full stereochemistry ([C@H], [C@@H], /, \) when it has any: the service compares structures on their canonical form, and a missing stereocentre makes a distinct monomer look like a duplicate of another one. Diethylglycine has no stereocentre, so there is nothing to add here.

See Attachment Points and CAP Groups for the other accepted notations and for CXSMILES.

Step 2: Open the form

On the Home page, click New Monomer. The Monomer management dialog opens with every field visible. The Definition and Structure tabs at the top show one half at a time; Show All is the default and is the easiest way to work.

The empty Monomer management dialog: Name, Polymer Type, Monomer Type, Natural Analog, Symbol, Author, the Chemical structure field with its Preview button, and an empty structure area

Step 3: Fill in the definition

Field	Deg example	Notes
Name	`Diethylglycine`	Required. Unique within your organisation for the polymer type.
Polymer Type	`PEPTIDE`	Required, preselected. Cannot be changed once created. Selecting it filters the two lists below.
Monomer Type	`Backbone`	Required. The list opens on `Branch`, so change it: `Backbone` for a residue that sits in the chain, `Branch` for one that hangs off a side chain.
Natural Analog	`X - Unknown/Any`	Required. The natural residue this monomer stands in for. A dialkyl glycine replaces no single natural residue, hence `X`.
Symbol	`Deg`	Required. Unique within your organisation for the chosen polymer type. Cannot be changed once created.
Author	your name	Optional free text.
Chemical structure	`CCC(CC)(N[:1])C([:2])=O`	SMILES or CXSMILES with `[*:n]` attachment points.

The meaning of each list, and which combinations exist, are described in Monomer Types, Polymer Types and Natural Analogs.

Step 4: Preview the structure

Click Preview, beside the Chemical structure field. The application draws the molecule with each attachment point labelled R1, R2, and so on, and one Cap Group selector per attachment point appears below the drawing.

The dialog after Preview: the diethylglycine drawing with R1 on the nitrogen and R2 on the carbonyl carbon, and the R1 Cap Group and R2 Cap Group selectors below it

Check three things on the drawing:

the skeleton is the one you meant;
the R labels sit on the right atoms;
the number of R labels matches the number of [*:n] in your SMILES.

If the message reads Invalid SMILES. Could not generate structure., the string is not parseable. Common causes are an unbalanced bracket or parenthesis, a lowercase aromatic atom outside a ring, or an attachment point written without a number. Fix the text and click Preview again.

Step 5: Set the cap groups

For each R-group, choose the cap group: the small group that completes the valence when this attachment point is not used in a chain. For a standard peptide monomer:

R-group	Cap group	Why
R1	`H - Hydrogen`	A free N-terminus is an amine, `NH2`.
R2	`OH - Hydroxyl`	A free C-terminus is a carboxylic acid, `COOH`.

Every selector opens on H, so set R2 Cap Group to OH - Hydroxyl for Deg. The vocabulary also offers NH2, Azide and Ethynyl. See Attachment Points and CAP Groups.

Preview resets the cap groups

Each click on Preview rebuilds the cap group selectors and puts them back to H. Set the caps after your last preview, just before you save.

Step 6: Create

Click Create. The service validates the structure, computes its canonical form, generates the drawing, and the dialog closes. The new monomer appears in the Home report with its structure, symbol, types and a Private status.

Four messages can stop the creation here:

Structure has changed. Please click Preview before saving. You edited the SMILES after the last preview. Preview again, then create.
Monomer with this structure is already registered: meG. If you expected a distinct structure, verify your input carries full stereochemistry … The same molecule already exists, here as the public monomer meG. Use that symbol instead. See Canonical SMILES and Duplicate Detection.
Monomer with this symbol is already registered: …, or Cannot modify protected public monomer '…' (public seed data). The symbol is taken, by one of your monomers or by a public one. Pick another symbol.
Registering 'Deg' corresponds to 1 deleted monomer (2504). Nothing was written. A monomer with this symbol or this structure was deleted earlier. Ask an Administrator to revive it from the Version Log rather than registering a second one. See Versioning and Deletion.

Editing a monomer: correcting a cap group

Suppose you registered N-methyl-norleucine as MeNle, previewed it, and clicked Create without going back to the cap groups. R2 was saved as H, so the free residue is an aldehyde and every peptide ending on it gets a wrong molecular weight.

On the Home page, click See on the MeNle row. The dialog opens with Symbol and Polymer Type locked; the other fields stay editable, and the cap group selectors show the saved values.
Set R2 Cap Group to OH - Hydroxyl. Do not click Preview, unless you also changed the structure; if you do, set the caps again afterwards.
Click Apply Changes.

The cap groups count as a material change, so the monomer's version number goes from 1 to 2 and the previous state is archived. An Administrator can see the before and after in the Version Log, with What changed reading R-groups; see How to Review a Monomer's Version History. Changing only the Name or the Author does not create a version.

The SMILES shown when you reopen a monomer is the normalised form computed by the service, not the text you typed. It is chemically the same molecule.

Deleting a monomer

Deleting is reserved to Administrators: the Delete buttons appear only for them. Click Delete on the Home report row, or in the dialog, and confirm. The confirmation reads Delete this monomer? It will disappear from the catalogue; a Monomer Administrator can restore it from the Version Log. The monomer disappears from the library, and its full state is archived so that it can be revived later. If the monomer still belongs to a monomer set, the deletion is refused with the list of sets to remove it from first. See Versioning and Deletion.