3vee molecular volume tools

Browser-based volume assessment and internal-volume extraction for PDB structures.

Calculations run locally with single-threaded WebAssembly. No coordinate upload server is used.

External volumes

Volume Calculation Calculate structure volume for a selected solvent-probe radius.

Volume Range Calculate structure volume across a range of probe radii.

Internal volumes

Channel Finder Find and extract major channels based on their size.

Single Channel Extraction Extract a channel near a known x, y, z coordinate.

Solvent Extraction Extract all solvent-accessible internal volume from a structure.

Exit Tunnel Extraction Extract the polypeptide exit tunnel from a 50S ribosomal subunit.

Volume Calculation

Voxel-based solvent-excluded volume and surface-area calculation for PDB coordinates.

Single-threaded WebAssembly; coordinate data and results remain in this browser.

Structure

RCSB accession or a local PDB coordinate file.

RCSB PDB ID Upload file

PDB ID ?

Four characters

Use biological assembly 1 ? Downloads the first RCSB biological unit instead of the asymmetric unit.

Parameters

Probe radius, voxel spacing, and coordinate-record filters.

Probe radius ? Å Radius of the spherical solvent probe. Grid spacing ? Relative to 0.50 Å, 0.40 Å uses about 2× and 0.25 Å about 6-8× as many voxels.

Include HETATM records ? Keep ligands, ions, and other non-polymer atoms. Exclude water molecules Applies when HETATM records are included. Fill internal cavities ? Include enclosed internal voids in the reported volume.

2LYZ presets:

64-million bounding-grid limit Use a coarser grid for larger structures.

Building the molecular volume...

Preparing the Volume calculation...

Volume results

Completed in entirely in this browser.

Drag to rotate. Scroll to zoom. Right-drag to pan.

Volume information

Volume ?
Surface area ?
Sphericity ?
Effective radius ?

Center of mass ?
Atoms
Filled voxels
Bounding-grid voxels
Grid dimensions
Grid spacing
Probe radius
Internal cavities ?

Download results

MRC density map (.gz) Gzip-compressed occupancy map; decompress if required by your viewer JSON report Parameters, statistics, dimensions, and origin Input PDB The exact structure used for this calculation

Calculation stopped safely