Protein Data Bank format

Codename: pdb

Contents

Import from PDB format

PDB files complying the PDB Contents Guide version 2.3 are processed by Marvin, though with some negligible limitations. PDB files produced by various 3rd party applications may not comply the PDB standard. Most of these files are also properly handled though there might be exceptions.
All covalent bonds in proteins and in nucleic acids are properly assigned, but hydrogen bonds, sulphur and water bridges, coordinated bonds are not recognised yet. Covalent bonds in hetero groups are perceived based on geometry, bond types are guessed with some errors. Hydregon atoms are identified and bonded to the appropriate heavy atom eiter in chains, in hetero groups as well as in water molecules.
Multiple models are properly processed as well as insertions and modified residues.

Import options can be specified in the format string. The format descriptor and the options are separated by a colon. Options listed below are available for PDB import.

H or +H Add explicit hydrogen atoms. Usage: "PDB:H"
-H Remove explicit hydrogen atoms. Usage: "PDB:-H"
c     Omit CONECT records for hetero compounds. Bonds are detected by the PDB reader modul based on local geometry unless the b option is specified. Usage: "pdb:c"
b     Do not recognise bond order. All bonds either defined by CONECT records or generated by PDB import are represented as ANY bonds. Usage: "pdb:b"

Limitations

Standard record types listed below are not recognised by the current version of PDB import:

The recognition and preper processing of these record types will be implemented in forthcoming releases on demand.

Export to PDB format

Marvin exports simplified PDB files containing record types listed below:

Export options can be specified in the format string. The format descriptor and the options are separated by a colon. Options listed below are available for PDB output.

H or +H Add explicit hydrogen atoms. Usage: "PDB:H"
-H Remove explicit Hydrogen atoms. Usage: "PDB:-H"
Limitations:

Reference