PDBx format!

I am sure this blog’s readers are aware of the PDB format. This format, created in the 1970s, is a standardized format for data derived from X-ray diffraction and NMR studies [1]. Until 2006, homology/theoretical models were also accepted for deposition, but not any more [2]. [See previous post on Protein Model Portal for submitting homology/theoretical models]

ResearchBlogging.orgThe current limit of PDB format is that a coordinate file with more than 62 chains and 99,999 atoms cannot be uploaded as a single file and hence was split into three or four separate PDB depositions. To overcome this limitation, a new format has been on the works and recently the working group announced the new format recommendations. [3, 4]

Not that I warned you. The first FAQ [4] on this link says:

What should every PDB user know about PDBx/mmCIF?
The PDB file format will be phased out in 2016.
PDBx/mmCIF will become the standard PDB archive format in 2014.

What is this new format?
To illustrate the changes, the first image is the ATOM records in the current PDB format. And, the second image is the PDBx format of the same information.

format1The new PDBx format:
format2Did you observe any changes? Here is a comparative image below that has the ATOM records aligned one below the other.
compareThe first thing that caught my eye was the order of the columns the new format is using. Also, the extra decimal positions for occupancy and B-factor columns. Now, if you look at the second image, we saw some extra lines before the ATOM records. These are the list of things in the “atom_site” category. The new format has the following categories and under each category, there is a detailed description of what goes into it. For example, the ATOM records is what is called as the ATOM_SITE category. Under this, there is information describing atomic positions.

PDB to PDBx correspondences

This link describes what items in PDB correspond to the new PDBx format

The website (http://mmcif.wwpdb.org/) and the FAQ have tons of information. Check it out, and get familiar with the new format of PDB! You have two years to learn it. 🙂


  1. http://www.rcsb.org/pdb/static.do?p=file_formats/pdb/index.html. Accessed: 2014-03-07. (Archived by WebCite® at http://www.webcitation.org/6NtpuqkvU)
  2. http://deposit.rcsb.org/depoinfo/depofaq.html. Accessed: 2014-03-07. (Archived by WebCite® at http://www.webcitation.org/6NtpzBByw)
  3. http://www.emdatabank.org/lrg_strct_dpstn.html. Accessed: 2014-03-07. (Archived by WebCite® at http://www.webcitation.org/6Ntq1KxKY)
  4. http://www.wwpdb.org/workshop/wgroup.html. Accessed: 2014-03-07. (Archived by WebCite® at http://www.webcitation.org/6Ntq3BY5u)
  5. http://mmcif.wwpdb.org/docs/faqs/pdbx-mmcif-faq-general.html. Accessed: 2014-03-07. (Archived by WebCite® at http://www.webcitation.org/6Ntq56e1O)

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