Class MMTFReader

All Implemented Interfaces:
GenericLineReader

public class MMTFReader extends MMCifReader
JmolData RCSB MMTF (macromolecular transmission format) file reader see https://github.com/rcsb/mmtf/blob/master/spec.md Note added 2024.01.19 Jose Duarte 2:03 PM (email) to MMTF-Users From July 2024 the PDB file archive will not be offered in the compressed MMTF format anymore. Users are strongly encouraged to switch to the BinaryCIF format, which has been available since 2020. Details on how to access BinaryCIF (BCIF) data files for the entire PDB archive are available here. RCSB PDB support is ready to assist with any issues or questions at info@rcsb.org. full specification Version: v0.2+dev (as of 2016.08.08) is implemented,including: reading atoms, bonds, and DSSP 1.0 secondary structure load =1f88.mmtf filter "DSSP1" [Note that the filter "DSSP1" is required, since mmtf included DSSP 1.0 calculations, while the standard for Jmol itself is DSSP 2.0. These two calculations differ in their treating of helix kinks as one (1.0) or two (2.0) helices.] reading space groups and unit cells, and using those as per other readers load =1crn.mmtf {1 1 1} reading bioassemblies (biomolecules) and applying all symmetry transformations load =1auy.mmtf FILTER "biomolecule 1;*.CA,*.P" reading both biomolecules and lattices, and loading course-grained using the filter "BYCHAIN" or "BYSYMOP" load =1auy.mmtf {2 2 1} filter "biomolecule 1;bychain";spacefill 30.0; color property symop Many thanks to the MMTF team at RCSB for assistance in this implementation.
Author:
Bob Hanson hansonr@stolaf.edu