MMTF News

ChemDoodle 3D v3 offers MMTF Support, May 2, 2017

The latest version of ChemDoodle 3D can read and write MMTF files, and can load them from URLs.

MMTF Workshop, San Diego, California, June 26-28, 2017

Structural Bioinformatics Training Workshop and Hackathon 2017: Application of Big Data Technology and 3D Visualization, San Diego Supercomputer Center, University of California, San Diego. Support for travel is available for a limited number of participants from non-profit organizations. Apply now! Application deadline April 30, 2017.

MMTF Specification Paper published, April 5, 2017

Bradley AR, Rose AS, Pavelka A, Valasatava Y, Duarte JM, Prlić A, Rose PW (2017) MMTF - an efficient file format for the transmission, visualization, and analysis of macromolecular structures. bioRxiv 122689; doi: https://doi.org/10.1101/122689

253rd ACS National Meeting, San Francisco, California, April 2-6, 2017

  • "Scalable web-based molecular graphics and visualization of structure quality metrics", by Alexander Rose

3D Coordinate Compression Paper published, March 31, 2017

Valasatava Y, Bradley AR, Rose AS, Duarte JM, Prlić A, Rose PW (2017) Towards an efficient compression of 3D coordinates of macromolecular structures. PLOS ONE 12(3): e0174846. doi: 10.1371/journal.pone.0174846

Postdoctoral Fellow Position Big Data/Structural Bioinformatics, February 24, 2017

Please see job description. Applications will be reviewed on a first-come first-served basis.

BD2K All Hands Meeting, North Bethesda, Maryland, November 29-30, 2016

  • "Compressive Structural Bioinformatics: Large-scale analysis and visualization of the PDB archive".
    Abstract | Slides

Postdoctoral Research Symposium, San Diego, California, November 1, 2016.

  • "MMTF, an ultrafast format for macromolecular data transmission".

Experimental MMTF load support in PyMOL v1.8.4

We are happy to announce that the release of PyMOL v1.8.4 has an experimental MMTF load support.

End of support for version 0.2 on November 1, 2016.

With the release of MMTF version 1.0 we will end support for version 0.2 on November 1st. Until then the wwPDB archive files are available at http://mmtf.rcsb.org/download.html and will be updated on a weekly basis for version 1.0 and 0.2. Please update your libraries as soon as possible. The latest versions of our Java, Python and JavaScript libraries support version 1.0. If you need more time updating please don't hesitate to contact us.

MMTF 1.0 released on August 15, 2016!

The MMTF project is pleased to announce the release of MMTF v1.0. MMTF is an open-source binary file format optimized for efficient transmittion and fast parsing of 3D structures of biological macromolecules.

Today MMTF ships with support for working with: The major feature added in this release includes the transformation matrices that describe noncrystallographic symmetry operations needed to create all molecules in the unit cell (see the changelog). In addition to the new changes, this release saw significant advancements in stability and usability:
Stability
We released MMTF 0.0.1 over four months ago (April 26, 2016). This extensive testing period enabled us to stress our server under a weekly update routine, find any issues that might impact the stability of converting mmCIF to MMTF, fix them, and confirm they were fixed. This all makes MMTF 1.0 our most stable release to date.
Usability
We designed MMTF to make it easy to incorporate to your projects. Our format is already supported by 3Dmol, MolSoft ICM v3.8-5 and Jmol v14.5.4 has a preliminary MMTF reader.

The 1.0 release represents a milestone where we believe MMTF is ready for general use. For more details, see specification of MMTF 1.0.

NII International Meetings, Shonan Village Center, Japan, September 5-8, 2016

  • "Web-based Molecular Graphics".

San Diego CADD Meeting, San Diego, California, August 30, 2016

Calit, Atkinson Hall, room 2004, San Diego, California, August 19, 2016, 10 - 11 am.

  • "Scalable 3D molecular graphics on the web" by Alexander Rose
Thanks to efforts of Maria Voigt from Rutgers, The State University of New Jersey, MMTF has a logo:

San Diego Bioinformatics Users Series (SDBUS), San Diego, California, August 12, 2016

Web3D Conference, Anaheim, California, July 22-24, 2016

Sequence-Structure Hackathon at ISMB Conference, Orlando, Florida, July 8-11, 2016

ISMB Conference, Orlando, Florida, July 8-12, 2016

3DSIG meeting, Orlando, Florida, July 8-9, 2016

  • “Small, fast and useful - MMTF a new paradigm in macromolecular data transmission”.
    Abstract | Poster

  • “Scalable 3D molecular graphics on the web”.
    Abstract | Slides | Poster

Bioinformatics Open Source Conference (BOSC), Orlando, Florida, July 8-9, 2016

MMTF 0.2.0 released

Version 0.2 got released to public! For more info see the specification or check the changelog.

MMTF 0.1.0 released

We are happy to announce the release of MMTF 0.1.0! This release includes Java and JavaScript API.