non-PDB format compatible entries
- too large (> 99,999 atoms)
- too complex (> 62 chains)
- chain ids with more than 2 characters
- complex sheet records(e.g. a large beta barrel structure)
- large B factor (≥ 1000)
- 5-character CCD IDs
As of December 10 2014, the previously split entries for a structure have been consolidated into a single large entry. The primary reason for the split entries was due to
the legacy pdb format not being able to handle the number of atoms and number and chains the consolidated entry would hold. However, the wwPDB has been dedicated to
migrate the PDB into a more future proof databank using the PDBx/mmCIF format. As such, the split entries have now been consolidated into a single entry and the individual
split entries have been obsoleted. New split entries will no longer be released and will only be released as a single consolidated entry.
Since many legacy software still is not able to process PDBx/mmCIF or PDBML files, the wwPDB has prepared a pdb-bundle so that legacy software can still load the new large structures.
The following software is known to be able to process PDBx/mmCIF files:
- molmil
- PDBj website (CIF file Tree viewer)
- jV
- Jmol/JSmol
- PyMol
- OpenBabel
- UCSF Chimera
- OpenRasMol
- Coot
- CCP4mg
For more details, please refer PDBx/mmCIF Software Resources.
Note that even though the above software is able to process PDBx/mmCIF files, due to the nature of the large entries, the above software might not be able to properly load the large entries. Furthermore, additional hardware (e.g. > 6GB of RAM) or software (64-bits version of the above programs) might be required.
