I was surprised as to how hard it was to find a reference on this among the docs.

Does the Protein Data Bank mmcif/pdb-x archival format use Angstrom to specify cartesian x,y,z coordinates of atoms or something else or abstract units (perhaps defined per each mmcif _data frame?

How is the origin of the grid calculated -- for crystallographers out there?

Thank you


1 Answer 1


From google I got this as first hit :

PDB_format_1992.pdf :

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Hopefully they keept the same Unit of measurement during the data/file format evolution/extension

It seems the case for mmcif Data Item _atom_site.Cartn_x :

enter image description here

Some history here :

The Protein Data Bank: a historical perspective , The Protein Data Bank


PY  - 1971
DA  - 1971/10/01
TI  - Crystallography: Protein Data Bank
JO  - Nature New Biology
SP  - 223
EP  - 223
VL  - 233
IS  - 42
SN  - 2058-1092
UR  - https://doi.org/10.1038/newbio233223b0
DO  - 10.1038/newbio233223b0
ID  - ref1
ER  - 

enter image description here

About the axis origin CHARMM-GUI has a nice introductory lesson to PDB format (see CRYTST1 Record Section) Lesson 1: Introduction to PDB Format

and stolen from the web, free part of an old book :

enter image description here

  • $\begingroup$ Thanks, pip. Missed the "angstroms" part when browsing through the spec. The paper and book references are very much appreciated. $\endgroup$
    – rtviii
    Commented Jan 22 at 19:15

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