Molecule World User Guide: Android
A molecular viewer for Android phones and tablets. Open a structure from a file or fetch one by ID, then explore it in 3D with multiple display styles, color schemes, and selection filters.
Android edition
Contents
1. Getting a structure on screen
You can load structures from local files or fetch them by ID. Everything you open or fetch collects in the app's library, with newly added structures at the top, and the app reopens your last-used structure when you return.
Open a local file
Tap the Files button to open the library, then import a structure from your device (Downloads, Drive, or anywhere the Android file picker can reach). Supported types are listed below; gzipped files are also accepted.
Fetch by PDB ID
From the library you can fetch a structure by its four-character PDB ID (e.g. 1ID3). It downloads from RCSB as a BCIF biological assembly, imports into your library, and loads — so large complexes still open quickly.
File types
Molecule World works with several structure formats:
| Format | Typical source | Notes |
|---|---|---|
PDB (.pdb) |
RCSB, hand-built files | Plain-text protein / nucleic acid structures |
CIF / mmCIF (.cif) |
RCSB, hand-built files | Modern plain-text structure format |
BCIF (.bcif) |
RCSB ModelServer | Biological and large structure assemblies |
MMDB JSON (.json) |
NCBI | Rich annotations (domains, etc.) |
SDF / MOL (.sdf) |
PubChem | Small chemicals |
PDB, CIF, BCIF, and files are also accepted gzipped (.gz).
2. Moving around in 3D
Molecule World uses standard touch gestures to manipulate structures.
| Gesture | Action |
|---|---|
| One-finger drag | Rotate the structure |
| Pinch | Zoom in / out |
| Two-finger drag | Pan |
| Auto-rotate (spinner) | Spin the structure hands-free |
A freshly loaded structure auto-rotates so you immediately see it in 3D. Tap the canvas — or the auto-rotate button — to stop the spin. Tapping the canvas also dismisses any open panel (Info, Color key, Help) in the same tap.
Molecule World remembers how you left each structure — style, colors, Show selection, and water toggle are saved per structure and restored next time you open it. Tap Reset (R) to return to first-load defaults: the format-default style, all atoms shown, and centered framing.
3. Display styles
Switch styles from the Style control at the bottom. Available representations:
- Spacefill — atoms at full van der Waals radius, bonds hidden. Shows overall shape and packing.
- Ball & Stick — atoms as spheres, bonds as cylinders. The general-purpose view.
- Tubes (licorice) — thin bonds only, no large joint spheres. Good for tracing connectivity and backbones.
- Ribbon (cartoon) — smooth secondary-structure ribbons: helices as rounded coils, β-strands as arrows. The standard protein view.
- Surface — a molecular surface skin over the structure.
- Wire Surface — the same molecular surface drawn as a wireframe mesh, so you can see the surface shape while still seeing what's underneath.
Heterogens (ligands, ions, cofactors) follow special rules so they always read clearly: organic heterogens render as element-colored sticks/tubes, and metals render as element-colored spheres at covalent radius — in every style, including ribbon and surface.
4. Color schemes
Coloring is independent of display style — pick any combination. Switching a color scheme is fast and doesn't reload the structure.
| Scheme | What it shows |
|---|---|
| Element (CPK) | Standard per-atom element colors (C, N, O, S…) |
| Secondary structure | Helix / sheet / coil |
| Chain | Each chain a distinct color |
| Rainbow | Gradient along the sequence (N→C terminus) |
| Residue type | RasMol / Shapely convention (amino-acid types; purines and pyrimidines for nucleic acids) |
| Residue | Each amino acid or nucleotide has a specific color |
| Charge | Positive / negative / neutral (nucleic backbones read negative) |
| Hydrophobicity | A hydrophobicity palette across residue types |
| B-factor | Blue-white-red gradient scaled to the structure's own B-factor range, highlighting areas of higher atomic motion or positional uncertainty |
| Domain | Structural domains — see section 6 |
In chain, rainbow, and other residue-level schemes, heterogens stay colored by element so ligands and ions remain identifiable. The color key notes this where it applies.
B-factor coloring is available for PDB, mmCIF/BCIF, and MMDB structures that carry B-factor (temperature-factor) data; it's dimmed for structures that don't — for example CN3D files, or predicted structures with no real per-atom variation to show.
5. Showing part of a structure
Use the Show selector to focus on a subset of the structure, or on a backbone representation. Everything outside the selection is hidden.
- All — the whole structure
- All + water — the whole structure including crystallographic waters (see below)
- Protein — amino-acid chains only
- Nucleic acids — DNA / RNA only
- Heterogens — ligands, ions, cofactors
- Core backbone — backbone trace
- Complete backbone — full backbone
- Cα trace — alpha-carbon trace
Water. Crystallographic waters are hidden by default. Choose All + water to draw them (as their oxygen atoms). The option is dimmed for structures that contain no water, and your choice is remembered per structure.
Dimmed options. Color schemes and Show items that don't apply to the loaded structure are dimmed and can't be selected — only the combinations that make sense for what you've opened stay active. For example, Heterogens is dimmed when a structure has none, Secondary structure when no helices or sheets are present, Nucleic acids when there are none, and B-factor when the structure carries no usable B-factor data.
6. Color by Domain
When a structure has multiple structural domains, a Domain color option becomes available. Each domain is shaded along a light-to-dark ramp within its chain, so the domain architecture is visible at a glance.
For antibodies, Molecule World also fetches named domains (VH, CH1, CH2, CH3, Vκ, Cκ, …) from NCBI's CD-Search service when you load the structure. This runs in the background; the legend shows progress, then labels each domain by name. Results are cached per PDB ID, and a re-fetch control refreshes them.
When a structure has many repeated chains (for example a viral capsid), the domain legend collapses them to a unique set of colors rather than listing every copy, so you see a handful of domains instead of hundreds.
7. The color key
The color key (palette button) shows what the current colors mean. It's filtered to what's actually visible — only the residues, elements, and heterogens present under your current Show selection appear, and categories like secondary structure only show up when the structure actually contains them, so the key stays relevant and sized to fit. It updates live as you change color scheme or Show filter.
For heterogens the legend splits metals and non-metals, uses standard SNFG colors for sugars and Modomics-style symbols for modified nucleotides, and falls back to a CPK "heterogens by element" key in the element-colored modes. Monoatomic ions are labeled by element symbol (Cd, Cl, Zn…).
8. Structure info
The info dialog ("i" button) shows metadata for the loaded structure — title, ID, atom count, and related details pulled from the file. A Help ("?") page summarizes the on-screen controls and gestures.
9. Tips & behavior
- Large structures may pause briefly while loading or when switching to ribbon/surface; a progress spinner appears for longer operations.
- Per-structure memory restores your last view automatically — use Reset (R) to return to the default display.
- Surface and ribbon recoloring is quick because the geometry is cached; only the colors change.
- Tap the canvas to dismiss any open panel (Info, Color key, Help) and to stop auto-rotate.
- Snapshot (camera button) saves a high-resolution image of the current view — with a transparent background, cropped tight to the structure — to your device's Photos / gallery.
Appendix — Power user notes
For users who want to know why the viewer draws what it draws, and how to get the most out of the data.
A. How heterogens and metals are drawn
Ligands, ions, and cofactors are handled separately from the polymer so they always stay legible:
- Organic heterogens are colored by element in every scheme and drawn as sticks/tubes — including in ribbon and surface modes, where the main chain is a ribbon and the ligand still appears as connected atoms.
- Metals are colored by element and drawn as spheres at covalent radius (not van der Waals), so a lone ion reads as a compact ball. Metalloids are grouped with metals so they stand out.
This is why a ligand keeps its CPK colors even when the protein is colored by chain, rainbow, or hydrophobicity.
B. Bonds and connectivity
- Coordination bonds (metal–ligand contacts) render as dashed lines; bonds within a single residue stay solid. Implausibly long links (which can arise from symmetry-duplicated partners in a biological assembly) are filtered out so they don't draw as long dashed lines across the structure.
- Disulfides are drawn with short side-chain stubs anchored to the backbone so the S–S link is visible in ribbon mode.
C. Color by Domain, in detail
Two levels of domain data feed this mode:
- Geometric domains from MMDB/JSON — available for those formats when a chain has more than one domain. Shaded light-to-dark per chain.
- Named domains from NCBI CD-Search (CDD) — fetched in the background at load. For antibodies this resolves real immunoglobulin domains: heavy (VH, CH1, CH2, CH3) and light (Vκ/Cκ, Vλ/Cλ).
Domain intervals match against residue ordinals, not author numbering, so gaps and insertions don't shift the boundaries. Named results cache by PDB ID; use re-fetch to refresh. The domain legend shows each distinct domain color once, even across repeated chains.
D. Selection semantics
Show is show-only: anything outside the selection is hidden, not greyed. The selection survives style and color changes, and the color key filters to match — only what's visible appears in the legend. Backbone tiers differ in scope (core vs complete), and Cα trace reduces a protein to its alpha-carbon path.
E. Large structures and level of detail
Very large structures degrade gracefully rather than stalling. Above a size threshold, ribbon mode drops to a coil trace with reduced tessellation for large memory savings, and geometry is built off the main thread so the interface stays responsive; a progress indicator shows for longer operations.
F. Surfaces
The molecular surface is a marching-cubes mesh, shared by both the solid and wire surface styles. Recoloring a surface is fast because the mesh is cached and only the colors are recomputed, and switching between solid and wire reuses the same cached mesh.
G. Where structures come from
Fetched files carry their provenance in the filename (e.g. 1ID3.rcsb.bcif). Structures fetched by ID come from RCSB as BCIF biological assemblies via the ModelServer endpoint, so large complexes open with full metadata. Local files of any supported type can be imported through the library.
H. View state
Each structure's view — style, colors, Show selection, and water toggle — is saved on the device and restored per structure the next time you open it; Reset (R) returns it to first-load defaults.
I. Snapshots
The snapshot path renders a high-resolution offscreen image with a transparent background, cropped to the structure, and saves it to your device's Photos / gallery, ready to share from there.
Abbreviations
The above text uses several abbreviations.
| Term | Stands for |
|---|---|
| B-factor | Temperature factor — a per-atom measure of positional uncertainty or thermal motion |
| BCIF | BinaryCIF — a compact binary encoding of CIF |
| Cα | Alpha carbon — the backbone carbon of an amino acid |
| CD-Search / CDD | Conserved Domain Database — NCBI's domain-identification service |
| CIF / mmCIF | Crystallographic Information File / macromolecular CIF — the modern text format for structures |
| CN3D | NCBI's legacy 3D structure format ("see in 3D") |
| CPK | Corey–Pauling–Koltun — the standard per-element atom coloring |
| DSSP | Dictionary of Secondary Structure of Proteins — the hydrogen-bond method used to assign helices and sheets |
| DWB | Digital World Biology |
| MMDB | Molecular Modeling Database — NCBI's structure database |
| PDB | Protein Data Bank — a repository of 3D structures |
| RCSB | Research Collaboratory for Structural Bioinformatics — operates the PDB |
| SDF | Structure-Data File — a small-molecule format (used by PubChem) |
| SNFG | Symbol Nomenclature for Glycans — the standard coloring for sugars |
| VdW | van der Waals — the atomic radius used for spacefill and surfaces |