Support for MMTF has arrived in MDAnalysis!

Macromolecular Transmission Format support

The upcoming 0.16.0 release of MDAnalysis will have support for MMTF! MMTF is a new format designed to provide compact, efficient and fast browsing of the Protein Data Bank. Support for MMTF within MDAnalysis is offered through reading locally stored MMTF files, or through fetching the file directly from the PDB archive through the new MDAnalysis.fetch_mmtf function.

import MDAnalysis as mda

# Load a local file
u = mda.Universe('myfile.mmtf')

# Or download directly from PDB by providing PBD id
u = mda.fetch_mmtf('3J3Q')

The performance of loading MMTF files is a large improvement over traditional ascii PDB files, with the above system of approximately 2.4M atoms taking under 10 seconds to load. The compressed format and efficient algorithms for storing the data mean that downloading structures will also require much less bandwidth, making this possible even on slow connections.

MMTF files can support many different models for a given structure and this is made available through the .models attribute of a MDAnalysis Universe. This provides a list of AtomGroup objects each representing a different model. These models are able to each have a different topology.

from __future__ import print_function
import MDAnalysis as mda

u = mda.fetch_mmtf('4P3R')

print("This file has {} models".format(len(u.models)))

# Iterate over all models
for model in u.models:
    # analyse each model!

# Select atoms in a given molecule
ag = u.select_atoms('model 4 and name Ca')

Finally, full interoperability between different formats is provided in MDAnalysis, allowing MMTF files to be written to any of our supported formats. For example to download a MMTF file and write out to Gromacs GRO file:

import MDAnalysis as mda

u = mda.fetch_mmtf('4AKE')

u.atoms.write('4ake.gro')

Trying this out today

These features will all be in the upcoming 0.16.0 release of MDAnalysis, but if you can’t wait for that, it is also possible to install the latest development version. For full instructions on how to install the development version, see our guide on installing MDAnalysis from source.

— @richardjgowers