How to Explore the Peptide Viewer

The peptide viewer is the interactive canvas of a SAR Slide. It draws the reference peptide's backbone, branches, bridges, and chemical objects, and lets you inspect the variants observed across all aligned peptides. This guide covers navigating the canvas, selecting monomers, working with regions, reading branches and bridges, expanding monomers, cyclizing, opening galleries, choosing how endpoints are summarized, and the display options.

Navigate the canvas

The toolbar (top of the canvas) controls layout and interaction:

Two sliders on the canvas control the linear layout: Monomers per line (across the top) sets how many monomers appear before the backbone wraps to the next line, and Gap between lines (down the right edge, in px) sets the vertical spacing between the wrapped lines.

Select monomers

Enter selection by clicking Select in the toolbar (or hold Ctrl while in Pan & Drag mode). A Selection Options panel appears with a Selection Mode toggle: Rectangle or Lasso.

You can build a selection in several ways:

• Click a monomer to select it.
• Hold Ctrl and click more monomers to add them to the selection.
• Drag on the canvas (rectangle or lasso, per the Selection Mode) to select a set at once.
• Click an empty area of the canvas without Ctrl to clear the selection.

With monomers selected you can, from the selection toolbar, create a region, cyclize the selection, expand/collapse the selected monomers, or keep only the selection variable.

Work with regions

A region groups positions (contiguous or not) so you can collapse them into a single pill, analyze them together, filter them, and show them as one gallery.

• Create a region by selecting monomers and choosing Create Region.
• Manage a region by right-clicking it:

The region context menu offers: rename (pencil), Show Gallery, Expand Region / collapse, Filter on the reference, Keep only this region variable, and Delete Region. Regions can be contiguous (for example Region 24 to 28) or discontiguous (for example Region 19 + 22). Auto-generated Branch and synergy regions are managed by the app.

Read branches and bridges

• Branches are drawn above the backbone with a red connector and a Branch label, as their own numbered chain. They are collapsed by default; expand a branch region to see its monomers.

A branch always hangs off the backbone residue's R3, but it can bond through either of its own two ends, and your HELM says which: 3:R3-1:R1 bonds through the branch's first residue (its N-terminal end), 3:R3-3:R2 through its last (its C-terminal end). The viewer follows that. The red connector lands on the residue that actually carries the bond, and the chain then grows away from it — rightwards for a first-residue attachment, leftwards for a last-residue one, instead of crossing back over its own backbone residue. A collapsed branch behaves the same way: the connector points at the square of the bonded residue rather than at the row's first square.

Alignment gaps padding a branch are not residues, so a branch whose first column is a gap still attaches through its first real residue. Where the structure does not say which residue carries the bond, the first one is assumed. None of this is configurable — it is read from the data. The one thing that overrides it is your own hand: a branch you have dragged stays where you put it.

• Bridges are colored arcs between two monomers, colored by type (disulfide, lactam, thioether, and so on — see the Legend tab). Bridges present only in other peptides (not the reference) are drawn dotted/faded and can be toggled with Include Non-Reference Bridges.

Some bridges are not a direct bond but run through a chemical linker — a chemical monomer whose two attachment points each bond to one of the bridged residues. Such a bridge is drawn as the same colored arc with the linker as a node at its middle:

• Expand it from the bridge's right-click menu to draw the linker's chemical structure with its two bridge bonds; collapse it the same way.
• Drag the node to reshape the bridge — the arc keeps its shape and follows, and the bridge's gallery stays anchored on the node. Like other manual adjustments, the drag is not saved with the layout and Reset Layout clears it.
• Clicking the node opens the bridge's gallery, exactly like clicking the arc.

The linker is not part of the bridge's identity: all bridges between the same two residues are drawn as one bridge, and its gallery shows one variant per flavour — each chemical linker, the direct bridge, and the peptides with no bridge there at all. The linker's name appears in the bridge tooltip, in gallery variant cards (whose bridge symbol carries a small box on its arc marking the linker), and in the peptide list's bridge badges and tooltips. A bridge that only other peptides carry shows its linker as a small dashed marker instead of a full node — hover it for the name — and only when every such peptide bridges through the same linker; with mixed flavours the arc is drawn bare and the gallery tells them apart.

Expand monomers

By default each monomer is drawn as a labelled shape. Expand it — from the selection toolbar, or Expand all monomers in the More menu — to draw its actual chemical structure in place.

An expanded monomer's free attachment points are drawn with the cap group the Biotoolkit Monomer Service declares for them, so a C-terminal residue reads as the carboxylic acid it is, and an unused side-chain attachment point (a lysine outside any bridge, for example) shows its cap rather than nothing. Attachment points that carry a real bond — to the next residue, to a bridge, to a chemical object — stay drawn as that bond, uncapped. A monomer whose cap group the service does not declare is drawn with an implicit hydrogen, as before.

Cyclize

For a run of monomers joined end-to-end by a bridge, you can lay them out as a ring:

• Select the run and choose Cyclize Selection, or use a bridge's Cyclize menu, or Cyclize All Bridges from the More menu.
• A bridge that runs through a chemical linker cyclizes too: the linker takes its own place on the ring, between the two residues it joins.
• For a macrocyclic peptide, switch the whole peptide to a circular layout with the Cyclic toolbar toggle.
• Reverse with Uncyclize / Uncyclize All.

Open galleries

Click a monomer, bridge, region, or chemical object to open a gallery — a small, draggable table of the variants observed at that element across all aligned peptides, with per-endpoint aggregated values (and deltas when hotspot analysis is on). Use the expand icon to open the enlarged gallery for charts and larger tables.

Choose how an endpoint is summarized

A gallery cell covers several peptides — every peptide carrying that variant at that position — so each endpoint needs a rule for reducing them to one thing to show. That rule is the endpoint's aggregation, and you set it per endpoint.

Open Settings → Endpoints, open the endpoint, and use the Aggregation row on its Details tab. The quicker route is in the gallery itself: the grey suffix after an endpoint's name in the property-label column ((max)) is a button, and it opens the same list.

For a numeric endpoint:

A text endpoint gets a shorter list, because a mean, a median, a histogram and a boxplot all need the distance between two values and text has none. Those four are not offered at all rather than greyed out:

The bar chart is drawn against the gallery's whole category list and ordered alphabetically, so a category keeps the same slot and the same color in every column of the row and you can read a row across; a category no peptide in that cell carries leaves an empty slot. Hovering a bar names the category and its count. Colors come from the endpoint's own value coloring when it is colored by unique values.

Configure display options

Open Settings → Display to control how the canvas is drawn.

• Color monomers by — Amino acid colors, Number of variants, Popularity (peptide count), Amino acid distribution, or Hotspot (when hotspot analysis is enabled).
• Display toggles — Show Empty Positions (gaps) with N/C-terminus options, Show Bridges (+ Include Non-Reference Bridges), Show Side Chemical Chains (+ Include Non-Reference Chains), Show Line Break Links, Show Position Indexes, Show N/C-Terminus Labels.
• Galleries Options — default monomers per page, property label width, monomer column width.

Color mappings for amino acids and bridge types are documented on the Legend tab.

Next steps

• How to Analyze Hotspots and Synergies
• How to Cluster Peptides
• Understanding Peptides in Ideation