Work in progress...

here is old documentation for reading MTZ only

MTZ reader in WebAssembly

The MTZ file format is used for the storage of reflection data -- the data from diffraction experiments in macromolecular crystallography.

This library is primarily intended for web-based molecular viewers.

It can read an MTZ file and transform map coefficients (reciprocal space) to a density map (real space).

It uses:

• C++ code from GEMMI (license: MPL 2.0), for handling MTZ files,
• PocketFFT (license: MIT) for discrete Fourier transform,
• and Emscripten to compile C++ to WASM + JS.

You can see this package in action on https://uglymol.github.io/view/

Source code → gemmi repo

Binaries → npm i mtz

Usage

The module is generated with Emscripten option MODULARIZE, which wraps everything into a function that invoked (once) gives the module:

var module = Gemmi();

To wait until the module is ready-to-use call a promise-like then method:

Gemmi().then(function(module) {
  mtz = module.readMtz(array_buffer);
  ...
  mtz.delete();
});

The readMtz function above takes ArrayBuffer with the content of an MTZ file and returns Mtz object with:

• cell -- object representing unit cell with properties corresponding to cell parameters (a, b, c, alpha, beta, gamma),
• calculate_map_from_labels(f_label: string, phi_label: string) -- calculates a map by transforming map coefficients from the requested columns; returns Float32Array (length == nx * ny * nz) representing density values on the grid,
• calculate_map(diff_map: Boolean) -- calculates a map with default labels:
  • FWT/PHWT or 2FOFCWT/PH2FOFCWT for normal map (diff_map===false),
  • DELFWT/PHDELWT or FOFCWT/PHFOFCWT for difference map,
• last_error -- contains error message if the functions above return null,
• nx, ny, nz -- dimension of the last calculated map (necessary to interpret the flat array as a 3D array),
• rmsd -- also a property of the last calculated map,
• delete() -- frees the allocated memory (inside the WebAssembly instance's memory).

calculate_map returns a map as a Float32Array view of the WASM memory. This view is invalidated when the next map is calculated, so you may want to make a copy.