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, cyclizing, opening galleries, and the display options.
Each viewer canvas is one SAR Slide — a tab in the report. Use the tabs to switch between slides, or Add SAR Slide to create a new one.
Navigate the canvas
The toolbar (top of the canvas) controls layout and interaction:
| Control | What it does |
|---|---|
| Linear / Cyclic | Switch between the linear (line-wrapping) layout and a circular layout. Cyclic is enabled for macrocyclic peptides. |
| Pan & Drag | Zoom and pan the canvas; drag monomers, chemical objects, and regions to reposition them. |
| Select | Enter selection mode (or hold Ctrl while in Pan & Drag). |
| Reset Layout | Restore node positions; the dropdown also offers Save Layout and Reset to Default Layout. |
| Clear All Position Filters | Remove any per-position variant filters. |
| More | Expand/Collapse all monomers, Cyclize/Uncyclize all bridges, Hide all galleries, and Download Image. |
| Settings | Open the SAR Report settings drawer (Data, Endpoints, Clusters, Filters, Display, Hotspot, Legend). |
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.
- 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.
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.
- 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.
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.
