Answers.Body: <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>
  
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Answers.Text: Thanks, pip. Missed the "angstroms" part when browsing through the spec. The paper and book references are very much appreciated.
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Answers.UserDisplayName: pippo1980
Body: <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>
  
Tags: <pdb><3d-structure><distance>
Title: Does the `mmcif/pdb` format store atomic coordinates in units of Ångstrom, nanometers or something else?
ThreadText: # 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
  
  
  ---
  
  ## 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](https://cdn.rcsb.org/wwpdb/docs/documentation/file-format/PDB_format_1992.pdf) :
  
  [![enter image description here](https://i.sstatic.net/nyNmb.jpg)](https://i.sstatic.net/nyNmb.jpg)
  
  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](https://mmcif.wwpdb.org/dictionaries/mmcif_pdbx_v40.dic/Items/_atom_site.Cartn_x.html) :
  
  [![enter image description here](https://i.sstatic.net/ZloIU.png)](https://i.sstatic.net/ZloIU.png)
  
  Some history here :
  
  [The Protein Data Bank: a historical perspective](https://journals.iucr.org/a/issues/2008/01/00/sc5004/sc5004.pdf) , [The Protein Data Bank](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC102472/pdf/gkd090.pdf)
  
  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  - 
  
  ```
  
  [![enter image description here](https://i.sstatic.net/P8nmu.png)](https://i.sstatic.net/P8nmu.png)
  
  About the axis origin CHARMM-GUI has a nice introductory lesson to PDB format (see ***CRYTST1 Record*** Section) [Lesson 1: Introduction to PDB Format](https://charmm-gui.org/?doc=lecture&module=pdb&lesson=1)
  
  and stolen from the web, free part of an old book :
  
  [![enter image description here](https://i.sstatic.net/4peth.png)](https://i.sstatic.net/4peth.png)
  
  > **Comments:**
  > **username_0**: Thanks, pip. Missed the "angstroms" part when browsing through the spec. The paper and book references are very much appreciated.  
  
  ---
  
  