Getting the most out of Protein Viewer Pro
Protein Viewer Pro pulls structures straight from the RCSB PDB and renders them in an interactive 3D viewer. This guide covers everyday search and viewing, plus the electrostatic surface tools, control panel, and high-resolution sharing added in version 2.2.
01Finding a Structure
Everything starts with a PDB ID or a keyword search — this part of the app hasn't changed.
- 1Search by ID or nameEnter a 4-character PDB ID (e.g.
4HHB) or a protein/gene name on the search screen. - 2Pick a resultTap a result to open it in the Main Viewer, where the structure loads and renders automatically.
- 3Go deeperFrom the viewer, use See more details to open the Analyzer screen for UniProt functional annotations.
02Main Viewer
The whole screen now scrolls as one unit — the 3D viewer, style controls, and PDB summary all stay reachable no matter your device's screen height.
Navigating the 3D view
Drag to rotate, pinch or scroll to zoom, and two-finger drag to pan. The viewer re-centers automatically whenever a new structure finishes loading.
Style & Color
Choose a rendering style — cartoon, stick, sphere, or line — and a color scheme (ssPyMol, chain, ssJmol, amino) from the chip rows above the summary. Changes apply instantly.
PDB Summary
Below the controls, the PDB Summary lists the structure's title, experimental method, resolution, and deposition/release dates. Since it scrolls together with everything else, it's now always reachable — including on smaller phone screens.
03Electrostatic Surface
A fast, client-side approximation of surface charge — useful for spotting charged patches and likely binding or interaction surfaces at a glance. It is not a Poisson–Boltzmann/APBS solve, but it's built on real CHARMM27 partial charges with Debye–Hückel screening.
- 1Turn it onTap the switch next to "Electrostatic Surface." A brief "Computing electrostatic surface…" status appears while the mesh builds, then the colored surface renders over the structure.
- 2Read the colorsRed tones mark negative potential, blue tones mark positive potential, and neutral areas stay close to the base surface color.
- 3Turn it offTap the switch again to remove the surface and fully restore the original structure style and color.
If a surface ever looks stuck or doesn't match the current view, tap the refresh icon next to the settings gear. It clears the surface, drops any cached charge data, and redraws the structure from scratch.
04Control Panel Reference
Tap the gear icon next to the Electrostatic Surface switch to open the settings sheet. Dragging a slider updates the label instantly; the surface itself rebuilds shortly after you stop dragging, so nothing overloads while you're adjusting.
| Control | Range | What it does |
|---|---|---|
| Surface opacity | 0.05 – 1.0 | How see-through the surface is. Lower values let the underlying structure show through clearly. |
| His charge | 0.0 – 1.0 | Histidine protonation state, from fully neutral (0) to fully protonated (1). Affects local charge near histidine residues. |
| Contrast (clamp) | 0.5 – 15.0 | Clamps the potential range used for coloring. Lower values exaggerate small charge differences; higher values compress them. |
| Debye length | 2.0 – 20.0 Å | Approximate screening distance for the electrostatic model — shorter values localize potential more tightly around charged residues. |
| Visual scale | 0.5 – 10.0 | An overall multiplier on computed potential before coloring, for fine visual tuning independent of the underlying physics settings. |
The Main Viewer opens with a bolder surface (opacity 0.55) for quick orientation. The Analyzer screen opens fainter (opacity 0.20) so the structure underneath stays clearly visible while you review functional features.
05Snapshot & Share
Capture exactly what's on screen — structure alone, or with the electrostatic surface applied — as a high-resolution PNG.
- 1Frame the viewRotate and zoom to the angle you want, and set up style, color, or electrostatic surface as desired.
- 2Tap the share iconIn the top-right of the app bar. The app briefly renders at higher resolution, then hands you the finished image.
- 3Save or send itThe share sheet covers saving to Photos/Gallery, AirDrop, Messages, email, and any other app that accepts images.
06Analyzer Screen
Reached via See more details on the Main Viewer, this screen pairs the same 3D viewer and electrostatic tools with UniProt functional annotations.
Feature list
Domains, active sites, and other UniProt-annotated regions are listed below the viewer. Tap one to highlight it directly on the structure.
Same electrostatic tools
The switch, settings gear, and reset button work exactly as on the Main Viewer — just tuned to a fainter default so annotated regions stay easy to see underneath.
07Tips & Troubleshooting
Large parameter changes recompute the whole surface mesh, which takes a moment on complex structures. Watch for the status message, or use Reset / redraw if it seems stuck.
Use the Reset / redraw icon next to the switch — it forces a full clean redraw of the base structure, clearing any leftover surface state.
Well-resolved, single-chain or small-complex structures give the cleanest surfaces. Very large assemblies take longer to compute.
08What's New in 2.2
- ✓Electrostatic potential surfacesNew on both the Main Viewer and Analyzer screens, with a full control panel.
- ✓Reset / redraw buttonOne tap restores the original structure at any time.
- ✓High-resolution snapshot & shareCapture and share publication-quality images directly from either viewer.
- ✓Reworked scrolling layoutStyle controls and the PDB Summary are now always reachable, on any screen size.