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== What is 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 ([https://www.redhat.com/archives/fedora-package-announce/2008-November/msg00262.html announcement]). | |||
Ubuntu users may install the package using apt-get: | |||
apt-get install libmmdb-dev | |||
For Apple machines, mmdb is available via [http://pdb.finkproject.org/pdb/package.php/mmdb The FINK project]. (Direct link to the Fink .info file [http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.4/unstable/main/finkinfo/sci/mmdb.info '''HERE''']). | |||
If you wish to compile the MMDB source yourself, you can obtain a standalone distribution tarball from [https://launchpad.net/mmdb The MMDB project on Launchpad] or from the [http://lmb.bioch.ox.ac.uk/coot/software/dependencies/ Coot software dependencies site] at Oxford. | |||
== How to use it? == | == 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 == | == Documentation == | ||
* [http://www.ebi.ac.uk/pdbe/docs/cldoc/ The author's documentation of MMDB] at the European Bioinformatics Institute | |||
* [http://www.ebi.ac.uk/pdbe/docs/cldoc/ CCP4 Coordinate Library Project] at the European Bioinformatics Institute |
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