Extra residue bonds present in MMTF data from v1.0.9.

[iclkevin]

I recently updated to v1.0.9 from v1.0.5 to gain access to the HTTPS ReaderUtils function. I noticed one particular file is now producing extra bonds: 3N4B. There are now a total of 4135 residue bonds produced, instead of the correct 4131. In the rendering, these bonds are incorrect. Everything else in the file appears correct. Any ideas on what the problem may be?

I do not know if the data has changed or if the issue is in a version of the Java MMTF libs >1.0.5 as I cannot test from v1.0.5 anymore with HTTP.

[josemduarte]

This sounds like related to this issue: rcsb/mmtf#44

Just tried and I think the display in pymol looks ok:

or am looking at the wrong thing?

Important note: mmtf is now under minimal maintenance. The preferred compressed format for PDB data now is BinaryCIF

[iclkevin]

Thanks, Jose. I will take a closer look when I get some time next week, although it is suspect that the issue is only present on 2 residues out of all. I will download the MMTF file locally and see if I get the same results between MMTF 1.0.5 and 1.0.9.

How much longer will the MMTF services be supported? Should we begin deprecating it?