The current official format for the Protein Data Bank is PDBx/mmCIF. However, there are many structural bioinformatics tools that accepts the legacy PDB format rather than PDBx/mmCIF format. Some mmCIF structures cannot converted to PDB format, including:
- Entries containing multiple character chain ids
- Entries containing > 62 chains
- Entries containing > 99999 ATOM coordinates
- Entries that have complex beta sheet topology
For these structures, the Best Effort/Minimal PDB files are provided by the PDB database instead. Unfortunately, not all best effort/minimal files are generated correctly in the PDB database. Moreover, there is no publicly available tool for the generation of Best Effort/Minimal files. To address this issue, we develop BEst Effort/Minimal (BeEM), the first open source implementation for the generation of Best Effort/Minimal file.
Although binary executables are available for Linux, Windows and Mac, it is recommended to compile the C++ program on your own operating system:
g++ -O3 BeEM.cpp -o BeEMExample usage:
BeEM example_input/3j6b.cifOutput files should be identical to those in example_output/3j6b-*.
On Linux, Mac and Windows Subsystem for Linux, BeEM read input files with and without gzip compression.
Best effort/minimal PDB format files contain only authorship, citation details and coordinate data under HEADER, AUTHOR, JRNL, CRYST1, SCALEn, ATOM, HETATM records.
The following PDB records are not included: OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, REVDAT, SPRSDE, REMARKS, DBREF, SEQADV, SEQRES, MODRES, HET, HETNAM, HETSYN, FORMUL, HELIX, SHEET, SSBOND, LINK, CISPEP, SITE, ORIGXn, MTRIXn, CONECT.
BeEM may optionally include SEQRES and DBREF.
Extended length CCD names (i.e., residue names with 5 characters) will be mapped to a set of reserved CCD IDs: 01 - 99, DRG, INH, LIG that will never be used in the PDB. In this case, a tab-delimited mapping file ligand-id-mapping.tsv will be provided to map reserved CCD IDs to extended length CCD IDs.
For residue sequence number with 5 or more characters, the first four characters occupies usual location for the residue sequence number, the fifth character will occupy the position of the insertion code, while the remaining charaters are discarded. A single chain with >99999 atoms are splitted into multiple Best Effort/Minimal files.
Another program, cifte is available to perform the reverse operation of converting PDB format files to mmCIF/PDBx format.
g++ -O3 cifte.cpp -o cifte
cifte input.pdb output.cifChengxin Zhang (2023) BeEM: fast and faithful conversion of mmCIF format structure files to PDB format. BMC Bionformatics, 24, 260.