Mmdb
What is mmdb?
MMDB is a macromolecular coordinate library, written by Eugene Krissinel primarily for use by CCP4 group. The Coordinate Library is designed to assist CCP4 developers in working with coordinate files.
The Library features work with the primary file formats of the Protein Data Bank (PDB), the PDB file format and the mmCIF file format.
The Library provides various high-level tools for working with coordinate files, which include not only reading and writing, but also orthogonal-fractional coordinate transforms, generation of symmetry mates, editing the molecular structure and some others. The Library is supposed as a general low-level tool for unifying the coordinate-related operations.
The Clipper-MMDB interface package provides an interface to allow MMDB models to interact with other types of crystallographic data as part of a structure solution application.
How to install mmdb?
The easiest way for users of Linux RPM based distributions is to install the Fedora 9 RPM package (announcement).
Ubuntu users may install the package using apt-get:
apt-get install libmmdb-dev
For Apple machines, mmdb is available via The FINK project. (Direct link to the Fink .info file HERE).
If you wish to compile the MMDB source yourself, you can obtain a standalone distribution tarball from The MMDB project on Launchpad or from the Coot software dependencies site at Oxford.
How to use it?
Link your application with ...
Examples for atom selections
What is the mmdb string for all atoms in the A conformation of residue 30 in the B chain? Answer: "//B/30/*:A"
The general syntax is:
/mdl/chn/seq(res).ic/atm[elm]:aloc
e.g. "/1/A/12-130/CA" selects the CAs of residues A12-A130
or
e.g. "//*/1-10" for residues 1-10 in all chains
Some further information about the selection syntax can be found on the pdbcur site http://www.ccp4.ac.uk/html/pdbcur.html#atom_selection.
Documentation
- The author's documentation of MMDB at the European Bioinformatics Institute
- CCP4 Coordinate Library Project at the European Bioinformatics Institute