Volumetric Data

TipWhat are Volumes?

Volumetric data includes electron density maps, cryo-EM maps, and other 3D grid-based data. Use volumes to show experimental data or visualize molecular surfaces at different density levels.

MolViewSpec supports loading and visualizing volumetric data alongside molecular structures, which is essential for structural biology workflows.

Common Volume Types

Electron Density Maps

X-ray crystallography electron density maps (2Fo-Fc, Fo-Fc difference maps)

Use cases: Validate structure fitting, show experimental evidence, highlight ligand binding

Cryo-EM Maps

Electron microscopy density maps

Use cases: Show large assemblies, validate model building, display experimental data

Other 3D Data

Custom grid-based data (electrostatic potentials, molecular orbitals, etc.)

Supported Formats

MolViewSpec can load volumetric data in these formats: - CCP4/MAP - Standard crystallography format - DX/OpenDX - Text-based grid format - DSN6 - Binary density format

Basic Volume Loading

Volume Parameters

Isosurface Type

  • type: "isosurface" - Surface at specific density level

Styling

  • isovalue: Density threshold (typically 0.5-3.0 for electron density)
  • color: Surface color
  • opacity: Transparency (0.0-1.0)

Example: Structure with Density

Multiple Contour Levels

Show different density levels with different colors:

Common Isovalue Ranges

Electron Density (X-ray)

  • 2Fo-Fc maps: 1.0 - 1.5 σ (blue, shows overall structure)
  • Fo-Fc positive: 2.5 - 3.0 σ (green, missing density)
  • Fo-Fc negative: -2.5 to -3.0 σ (red, extra density)

Cryo-EM Maps

  • Main map: 0.5 - 2.0 (varies by map quality)
  • High confidence: 3.0+ (well-resolved regions)

PDBe Integration

PDBe provides electron density maps for X-ray structures:

Styling Tips

For Publication Figures

  • Use lower opacity (0.2-0.4) for clarity
  • Use muted colors (light blue, light grey)
  • Consider single contour level to reduce visual clutter

For Analysis

  • Use higher opacity (0.5-0.7) for better visibility
  • Use contrasting colors for different maps
  • Show multiple contours to assess density quality

Performance Considerations

WarningLarge Volume Files

Volumetric data files can be very large (100+ MB). Consider: - Using binary formats (CCP4, DSN6) instead of text (DX) - Cropping maps to regions of interest before loading - Adjusting isovalue to reduce surface complexity

See Also