douweschulte / pdbtbx

A library to open/edit/save (crystallographic) Protein Data Bank (PDB) and mmCIF files in Rust.

Home Page:https://crates.io/crates/pdbtbx

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Standardize precision of floating points in mmCIF output

douweschulte opened this issue · comments

  • PDB itself servers files that have occupancy of 1.00, it should be easy enough to put at least a point and one digit after that;
  • The above goes even for xyz coordinates, some of them outputted without a dot.
  • 16 digits after the dot in coordinates... Excessive precision is being frowned upon in the community when it comes to reporting in e.g. "Table 1". This implies that all the digits are meaningful. Writing out 16 digits in coordinates makes the precision of 1e-26 meters. Proton size is ~1e-15 meters (from Wiki). Let alone every digit and every whitespace to format them nicely is 1 byte on the disk.

(thanks to Oleg for raising the issue!)

I would propose to have a minimum of 1 decimal and a maximum of 5 decimals.