Both file formats are advertised as more memory/parsing efficent than old PDB format and its successor mmCIF format, but I can't understand the context (I'm a developer, but pretty new to the field of bioinformatics).

Is BinaryCIF a later iteration of MMTF concepts/ideas (so it's a new competing format) or is the purpose of the two formats different ?

Refs :


So binaryCIF is newer and is heavily inspired by MMTF.

NGL, the most "loved" JS library (IMO) to show protein fetches proteins as MMTF, while Mol* uses bCIF —Mol* has the official repo of the bCIF format. Alex Rose, developed the former at the RCSB PDB, and the latter in collaboration with the PDBe. He also worked with Antony Bradley, the main author on the MMTF format, who left the RCSB PDB, some 4+ years ago. So there is definitely no competition there.

  • The MMTF download of the RCSB works well: https://mmtf.rcsb.org/download.html
  • The MMTF format did not catch on —okay, mmCIF is only slowly replacing PDB, which is still the only accepted format for analyses—, hence the need for a bCIF format
  • The libraries to do the conversion aren't without glitches
  • In the distant future bCIF will be the sole binary format
  • mmCIF <--> bCIF conversion is easier

However, I really ought to stress that mmCIF is a better choice to bCIF or mmTF. And even then many tools still hate mmCIFs and use PDB format. If memory footprint is not really a problem, then stick with mmCIF. If you are running a webserver, you may be sending data as gzipped making this a moot point.

  • $\begingroup$ Good post. As stated, pdb (from the age of Fortran) remains a strong favourite $\endgroup$ – M__ Nov 7 '20 at 21:15
  • $\begingroup$ Thanks a lot for this useful and detailed response : a lot of context, exactly what I needed. We'll use MMTF essentially to send files to NGL (as you have guessed ;) ), internally our tools will work with PDB and mmCIF. I'll keep an eye on bCIF, as Mol* has impressive tools (but not needed at our current stage). Have a nice day and thanks again ! $\endgroup$ – ashas Nov 9 '20 at 8:20
  • $\begingroup$ Last year for my site, michelanglo, I was faced with a similar dilemma. Mol* has dotted lines for gaps and does not crash the browser with a virus or someone wanting to show hyperball representation on all residues. However, it was not documented (and then glitchy) so I firmly stuck with NGL, which is excellent. For file formats, I stick with PDB and a metadata dictionary as I know the format well and is despite having the jankiest syntax and no real metadata support (REMARK... ha!), does not break isopetides, disulfides or for no apparent reason. $\endgroup$ – Matteo Ferla Nov 9 '20 at 18:03

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