title: The Ensemble/Legacy Chimera extension: standardized user and programmer interface to molecular Ensemble data and Legacy modeling programs.
abstract: Ensemble/Legacy is a toolkit extension of the Object Technology Framework (OTF) that exposes an object oriented interface for accessing and manipulating ensembles (collections of molecular conformations that share a common chemical topology) and driving Legacy programs (such as MSMS, AMBER, X-PLOR, CORMA/MARDIGRAS, Dials and Windows, and CURVES). Ensemble/Legacy provides a natural programming interface for running Legacy programs on ensembles of molecules and accessing the resulting data. Using the OTF reduces the time cost of developing a new library to store and manipulate molecular data and also allows Ensemble/Legacy to integrate into the Chimera visualization program. The extension to Chimera exposes the Legacy functionality using a graphical user interface that greatly simplifies the process of modeling and analyzing conformational ensembles. Furthermore, all the C++ functionality of the Ensemble/Legacy toolkit is "wrapped" for use in the Python programming language. More detailed documentation on using Ensemble/Legacy is available online (http:¿picasso.nmr.ucsf.edu/dek/ensemble. html).
authors.affiliation: Graduate Group in Biophysics, UCSF 94143-0446, USA.
authors.forename: D E
authors.initials: DE
authors.lastname: Konerding
mesh_terms: D003196:Computer Graphics; D008968:Molecular Conformation; D012984:Software; D013816:Thermodynamics; D014584:User-Computer Interface