How to Manage Your Organisation's Cap Groups

This guide shows how to add a cap group your chemistry needs, and retire a cap group you no longer want offered. For what a cap group is and why the choice matters, see Attachment Points and CAP Groups.

Prerequisites: the Administrator role in Biotoolkit Monomers. The Cap groups entry appears in the navigation menu, under Administration, only for Administrators.

Step 1: Open the Cap groups page

In the navigation menu, open Administration and click Cap groups. The page lists every cap group your organisation can use:

the Public ones, shipped with Biotoolkit and read-only, marked System in the By column;
your organisation's Private ones, with the account that last changed them.

The Scope chips (All, Private, Public) and Status chips (All, Active, Inactive) narrow the list, and the search box finds a symbol or a name.

The Cap groups page: the five public cap groups, then the organisation's private ones, Br, Cl, I and the new Propynyl, with the Scope and Status chips above the report

Your private cap groups are visible to your organisation only. Another organisation never sees them, and cannot use them in its monomers or imports.

Step 2: Add a cap group

Click New cap group and fill in the dialog:

Field	What to enter
Symbol	The name curators choose in the monomer form and write in import files, such as `Propynyl`. At most 50 characters, without a comma, a semicolon or a colon (an import file reads `R1:Propynyl`). It must not already be one of your organisation's cap groups, nor a public one such as `OH`, in any case.
Name	The readable name shown next to the symbol, such as `Propargyl`.
SMILES template	The cap's structure, with its attachment point written `[*:{n}]`, exactly once, and no space. `{n}` becomes the R-group number when the cap is applied.
Description	Optional: when to use this cap.
Display order	Optional: the cap's position in the monomer form's selector. Without one, it comes after the ordered caps.
Active	On: the cap is offered at once.

As you type the template, the preview draws the cap on R1 and checks it. Valid structure, one attachment point means the template is ready; otherwise the preview names the problem, such as a template with no attachment point or with two.

The New cap group dialog for Propynyl: symbol, name Propargyl, a propargyl template drawn on R1 with "Valid structure, one attachment point", a description, and the Active switch on

Click Create. The cap group is listed as Private and Active. Curators of your organisation can choose it at once for an R-group on the monomer form, and write it in an import file as R1:Propynyl. The Biotoolkit services that compute structures from your monomers pick it up within a minute.

The symbol cannot be changed afterwards: monomers and import files refer to the cap by it. To use another symbol, add a new cap group and retire the old one.

A public cap group cannot be replaced. To cap with another structure than a public cap gives, add a cap group with a symbol of its own, such as OMe rather than a second OH: public monomers name their caps by symbol, so a private OH would change their structure for your organisation. Click the symbol of a public cap group to read its template and the number of your organisation's monomers that use it.

Step 3: Change or retire a cap group

Click the symbol of one of your private cap groups, or its pencil in the Actions column, to open it. You can change everything except the symbol, then click Save changes.

To stop offering a cap group, switch Active off and click Save changes. The cap leaves the monomer form's selector, and an import that names it is refused. Monomers that already use it keep their structure, and you can switch it back on at any time.

Step 4: Delete a cap group nobody uses

The dialog of a private cap group says how many of your organisation's monomers use it.

No monomer of your tenant uses this cap. The Delete button is available. Click it and confirm. An import that names the symbol is then refused.
One or more monomers use it. The dialog offers no Delete, and says A cap in use cannot be deleted: deactivate it to retire it. Switch Active off instead, as in step 3.

A cap group in use cannot be deleted because its monomers would keep naming a cap group that no longer exists. Worse, a cap group added later under the same symbol, with another template, would silently give those monomers' caps another structure. Deactivating avoids both, and stays reversible.