The OpenMMS Toolkit

Corba and Relation Database Software
for Macromolecular Structure



General Info    News    Documentation    Downloads    Data

Support

Please note that OpenMMS is no longer being supported by the RCSB PDB. However, OpenMMS can be discussed on the OpenMMS Users Group's web site or email list.

General Information

The Protein Data Bank (PDB) has as its mandate full and effective use of macromolecular structure (MMS) information to further our understanding of biological systems. This mandate includes standards and software for effective use of biological data. To this end the PDB has initiated, developed and promoted a Corba standard for macromolecular structure ( OMG specification formal/2002-05-01) and developed OpenMMS software to exploit that standard. The National Partnership for Advanced Computational Infrastructure (NPACI) has helped support this development.

The OpenMMS Toolkit contains software for parsing protein and nucleic acid macromolecular structure data stored in the standard mmCIF format. The toolkit also contains software for loading the mmCIF data files into a relational database, and for running a Corba server to deliver binary MMS data directly over a network connection to applications. The translation into the different formats is driven by a central metamodel based on the ontology contained in the mmCIF dictionary. All of the software for the metamodel and for generating the translated expressions is written in Java and is included with the distributions.

The name of the "Full Release" OpenMMS distributions below identify both the Release Number of the distribution and the Model Name that was used in compiling the distribution. For example, the filename "OpenMMS-1.0.6_LSR-1.0.tar.gz" identifies the release number as "1.0.6" and the Model Name as "LSR-1.0". This same identifier string is also the name of the top-level directory created when the distribution is untar'ed.

The "Source Only" distributions listed below contain all the source code but have never been compiled. These distributions have file names with the pattern "OpenMMS-x.y.z_SourceOnly.tar.gz" and have not been built for any particular Model and do not contain any Java class files or metamodel derived information.

All distributions contain a README.html and COPYRIGHT.html file in the top-level directory. A Documentation_Index.html file in the docs subdirectory contains pointers to all of the documentation included with the distribution.


News

Native mmCIF Data File Rollout

For the next few months during the mmCIF data file rollout transition period, two types mmCIF files will be available from RCSB. The older "converted" mmCIF files were automatically generated by a conversion program from the legacy PDB data files. Unfortunately, these converted files often contain missing data fields and should not be used with the OpenMMS software since the missing fields cause mmCIF-parse errors.

When using the OpenMMS, it is highly recommended that users download the newer "native" mmCIF data files. These files are available at the RCSB PDB production FTP archive at ftp://ftp.rcsb.org/pub/pdb/data/structures/divided/mmCIF

Version 1.2 Released

Version 1.2 of OpenMMS is now available. This version includes a Corba server based on an OpenMMS relational database backend, models that include the pdbx exchange dictionary, and miscellaneous bug fixes. Note that version 1.2 uses the Corba Portable Object Adapter and therefore requires the Java 1.4.0 (or later) runtime environment.


Online Documentation

Latest Release
Documentation Index for OpenMMS-1.5.1_Std

Downloads

Precompiled Downloads

Latest Release
OpenMMS-1.5.1_Std.tar.gz
Previous Releases
OpenMMS-1.3.4_Compact.tar.gz
OpenMMS-1.2.12_LSR-1.0.tar.gz
OpenMMS-1.1.1_LSR-1.0.tar.gz
OpenMMS-1.0.6_LSR-1.0.tar.gz

Source Only Downloads

Latest Release
OpenMMS-1.5.1_SourceOnly.tar.gz
Previous Releases
OpenMMS-1.3.4_SourceOnly.tar.gz
OpenMMS-1.2.12_SourceOnly.tar.gz
OpenMMS-1.1.1_SourceOnly.tar.gz
OpenMMS-1.0.6_SourceOnly.tar.gz

mmCIF Data

mmCIF Data File FTP Site


OpenMMS was designed and written by Dr. Douglas S. Greer
San Diego Supercomputer Center / The University of California, San Diego.
9500 Gilman Drive, La Jolla, CA 92093, USA
Copyright © 2001, 2002, 2003     All Rights Reserved.