jRama Web Viewer

From the Bax Group at the National Institutes of Health ...

jRAMA:

A Web-Based Viewer for Inspecting TALOS-N Predictions

Load ▾ groups file, folder, PDB and project import. Load files… accepts individual pred*.tab files or one .zip bundle containing them. If a browser blocks local files or folders, approve the file picker prompt, or use Load files… as a fallback. More tips are in Help & FAQs.

Help & FAQs

Using the jRama Web Viewer

This panel adapts the original jRama help page for the current HTML / JavaScript viewer. The classic workflow of loading TALOS results, inspecting residues, toggling database matches and exporting restraints is preserved, but the old Java-applet setup steps are no longer required.

Quick start

Open the Load ▾ menu and choose Load files… or Load folder… to select your TALOS-N output tables, or choose one .zip archive that contains the pred*.tab files.
Click a residue in the Sequence panel to update the Ramachandran map and the linked charts.
Hover data points for tooltips; click a Rama database-match square or a bar in Secondary Shift to toggle W.
Use the classification buttons below the Rama plot to set Good, Bad, Ambiguous, Dynamic or Unclassified.
Optionally load a reference .pdb file to display the experimental φ/ψ marker in blue.
Use Save Project to store your edits to JSON, or use Data Viewer to inspect and download the edited tables.

If local-file access is blocked

This build is designed to open directly from index.html. If a browser blocks file or folder loading, open the Load ▾ menu, retry the needed action and approve the browser file-picker or permission prompt. If folder access is unavailable, use Load files… instead of Load folder…. You can also select a single .zip archive containing the pred*.tab files with Load files…. On managed Microsoft Edge installations, file-selection dialogs can also be disabled by policy.

On macOS, if Chrome, Safari, Edge or another browser cannot see files in Desktop, Documents, Downloads or iCloud Drive, open Apple menu → System Settings → Privacy & Security → Files & Folders and enable access for that browser, then retry the Load button. If macOS shows an Allow / Don’t Allow dialog for iCloud Drive or another file provider, click Allow.

Files you can load

File	Status	Purpose
`pred.tab`	Required	Main prediction summary used for the residue list, classifications, averaged φ/ψ values and exports. If `predS2.tab` is absent, its `S2` column also drives the RCI plot.
`predAll.tab`	Strongly recommended	Best-match database entries for the Rama plot; required for interactive `W` toggling and re-averaging.
`predS2.tab`	Optional	Dedicated RCI / S2 table. When present, it is preferred for the S2 plot; otherwise the S2 column from `pred.tab` is used.
`predABP.tab`	Optional	Q(ANN) / ANN surface overlay in the Ramachandran panel.
`predSS.tab`	Optional	Legacy combined secondary-structure / motif table used for the Structure & Motifs panel when no separate MICS table is present.
`predMICS.tab`	Optional	Separate MICS structural-motif table. When present, it restores the beta-turn motif plots and also supplies the structure probabilities used by Structure & Motifs.
`predAdjCS.tab`	Optional	Secondary chemical-shift distribution panel and linked residue-match highlighting.
`predChi1.tab`	Optional	Chi1 rotamer plot, shown at the bottom of the Structure & Motifs panel.
`results.zip`	Optional convenience	Select one standard `.zip` archive containing the `pred.tab` files with Load files…*. If ZIP import is unavailable in your browser, unzip locally and select the individual tables instead.
`reference.pdb`	Optional	Experimental backbone φ/ψ marker shown as a blue point in the Rama plot.
`*.jrama.json`	Optional	Saved project bundle that restores loaded tables, reference PDB content and your edits.

Main interactions

Ramachandran panel

Click a red or green database-match square to toggle whether that entry contributes to the averaged prediction. The viewer immediately recalculates circular means and deviations and updates the editable tables in memory.

Sequence panel

Each residue button carries the current TALOS class color. Clicking a residue updates the Rama plot, S2 / SS / MICS motif charts, Chi1 plot and the secondary-shift panel.

Structure & Motifs

The S2, secondary-structure, MICS motif and Chi1 plots share a linked vertical crosshair while hovering, so the same residue position is easy to compare across the stacked plots.

Secondary Shift panel

Hovering a bar highlights the corresponding TALOS match and shows its tooltip context; clicking the bar toggles the same W flag used in the Rama plot.

Data Viewer and exports

The Data Viewer shows the current table text after your edits. Export buttons generate XPLOR-NIH or CYANA torsion-angle restraints directly from the current predictions.

What changed from the original Java page?

No Java applet, browser plug-in, security exception list or local Python server is needed.
The landing view and residue-specific Ramachandran backgrounds use SVG assets.
The modern browser UI keeps the original multi-window layout while adding project save/load and an embedded help panel.
The classic Chi1 window is now integrated into the Structure & Motifs panel.

FAQs

Do I need every TALOS file?

No. pred.tab is the core input. The other files progressively enable the match list, surface overlay, structure charts, the separate MICS motif plots (predMICS.tab), secondary-shift distribution and Chi1 plot. Those same tables can also be supplied as a single .zip bundle through Load ▾ → Load files….

How do I preserve my edits?

Use Save Project to write a JSON bundle, or download the edited tables from the Data Viewer.

What do the classification buttons change?

They update the current residue class in the loaded prediction table and immediately refresh the Sequence button color and the on-screen state.

Where did the old Java browser instructions go?

They are historical. The original page described launching a Java applet and enabling Java in older browsers; this HTML / JavaScript port no longer needs any of those steps.

jRama Web Viewer

Load TALOS output files to begin.

Tip: click a red/green database match square in the Rama plot to toggle W and re-average.

Sequence

Predicted Secondary Structure and Motifs

Predicted RCI S2 value

Predicted Secondary Structure

Predicted Chi1 Rotamer [g-|g+|t]