<p>From google I got this as first hit :</p>
<p><a href="https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1992.pdf" rel="nofollow noreferrer">PDB_format_1992.pdf</a> :</p>
<p><a href="https://i.sstatic.net/nyNmb.jpg" rel="nofollow noreferrer"><img src="https://i.sstatic.net/nyNmb.jpg" alt="enter image description here" /></a></p>
<p>Hopefully they keept the same Unit of measurement during the data/file format evolution/extension</p>
<p>It seems the case for <code>mmcif</code> <a href="https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.Cartn_x.html" rel="nofollow noreferrer">Data Item _atom_site.Cartn_x</a> :</p>
<p><a href="https://i.sstatic.net/ZloIU.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/ZloIU.png" alt="enter image description here" /></a></p>
<p>Some history here :</p>
<p><a href="https://journals.iucr.org/a/issues/2008/01/00/sc5004/sc5004.pdf" rel="nofollow noreferrer">The Protein Data Bank: a historical perspective</a> , <a href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/pdf/gkd090.pdf" rel="nofollow noreferrer">The Protein Data Bank</a></p>
<p>AND :</p>
<pre><code>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  - 
</code></pre>
<p><a href="https://i.sstatic.net/P8nmu.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/P8nmu.png" alt="enter image description here" /></a></p>
<p>About the axis origin CHARMM-GUI has a nice introductory lesson to PDB format (see <em><strong>CRYTST1 Record</strong></em> Section) <a href="https://charmm-gui.org/?doc=lecture&amp;module=pdb&amp;lesson=1" rel="nofollow noreferrer">Lesson 1: Introduction to PDB Format</a></p>
<p>and stolen from the web, free part of an old book :</p>
<p><a href="https://i.sstatic.net/4peth.png" rel="nofollow noreferrer"><img src="https://i.sstatic.net/4peth.png" alt="enter image description here" /></a></p>

CC BY-SA 4.0
2024-01-22T19:15:51.220Z
Thanks, pip. Missed the "angstroms" part when browsing through the spec. The paper and book references are very much appreciated.
rtviii
CC BY-SA 4.0
2024-01-21T12:48:34.247Z
2024-01-21T15:16:13.407Z
2024-01-21T15:16:13.407Z
pippo1980
<p>I was surprised as to how hard it was to find a reference on this among the docs.</p>
<p>Does the Protein Data Bank <a href="https://mmcif.wwpdb.org/" rel="nofollow noreferrer">mmcif/pdb-x</a> archival format use Angstrom to specify cartesian x,y,z coordinates of atoms or something else or abstract units (perhaps defined per each <code>mmcif</code> <code>_data</code> frame?</p>
<p>How is the origin of the grid calculated -- for crystallographers out there?</p>
<p>Thank you</p>

<pdb><3d-structure><distance>
Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?
# Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?

(Asked by: username_0 on 2024-01-20)

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](https://mmcif.wwpdb.org/) 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

**Tags:** pdb, 3d-structure, distance

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## 1 answers

### Answer by username_1 on 2024-01-21. Score: 4 | Accepted answer

From google I got this as first hit :
PDB_format_1992.pdf :

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 :

Some history here :
The Protein Data Bank: a historical perspective , The Protein Data Bank
AND :
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  - 


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 :

> **Comments:**
> **username_0**: Thanks, pip. Missed the "angstroms" part when browsing through the spec. The paper and book references are very much appreciated.  

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