Mmdb: Difference between revisions
(Added working link to mmdb documentation as provided by Gerard Kleywegt on ccp4-dev.) |
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Link your application with ... | 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" | 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 | |||
== Documentation == | == Documentation == | ||
* http://www.ebi.ac.uk/~keb/cldoc/ and http://msd.ebi.ac.uk/~keb/cldoc/ are both broken. | * http://www.ebi.ac.uk/~keb/cldoc/ and http://msd.ebi.ac.uk/~keb/cldoc/ are both broken. | ||
* [http://www.ebi.ac.uk/pdbe/docs/cldoc/ CCP4 Coordinate Library Project] at the European Bioinformatics Institute | * [http://www.ebi.ac.uk/pdbe/docs/cldoc/ CCP4 Coordinate Library Project] at the European Bioinformatics Institute | ||
Revision as of 09:44, 16 November 2010
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 distros is to install the Fedora 9 RPM package (announcement). For Apple machines, this would probably be http://pdb.finkproject.org/pdb/package.php/mmdb .
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
Documentation
- http://www.ebi.ac.uk/~keb/cldoc/ and http://msd.ebi.ac.uk/~keb/cldoc/ are both broken.
- CCP4 Coordinate Library Project at the European Bioinformatics Institute