All of our software distributions come with full source code. Licensing terms vary with the package. The available packages are:
- Chimera
- extensible molecular modeling system
- MidasPlus
- molecular visualization
- PDB record I/O libraries
- read/write PDB files
- KSDSSP
- compute protein secondary structure
- Virtual sphere
- 3D manipulation with a mouse
- Object Technology Framework
- C++ molecular class generator
- NMR data analysis software
- NMR computation and visualization
- SGI OpenGL stereo software
- automatically switch SGI stereo mode
- DMS
- compute molecular surfaces
MidasPlus (Molecular Interactive Display and Simulation) is used extensively for the display and manipulation of macromolecules. Features of MidasPlus include the selective display of protein and nucleic acid structures, display of several types of molecular surfaces including van der Waals, solvent accessible, and space filling images with shadows, ability to depict protein secondary structure using "ribbon" drawings, viewing of images in three dimensions using stereo glasses, and easy interactive adjustment of various viewing parameters.The last release of MidasPlus (version 2.1) was made in November 1997. Although this version is still available, no additional releases are planned. Our Chimera extensible molecular modeling system has supplanted Midasplus.
We have open source versions of two libraries for reading and writing Brookhaven Protein DataBank (PDB) formatted files. One library is written in the C programming language, and other in the C++ programming language. Each can parse a PDB record (one line) into a structure, and output a PDB record from a structure.Also available is an electronic poster with a description of the scene annotations to PDB files that the above libraries support. The full paper describing the annotations has been published in the Journal of Molecular Graphics 13, 3 (June 1995).
ksdssp is an open source implementation of the algorithm described in Wolfgang Kabsch and Christian Sander, "Dictionary of Protein Secondary Structure: Pattern Recognition of Hydrogen-Bonded and Geometrical Features," Biopolymers, 22, 2577-2637 (1983).The package is distributed in C++ source code form and uses the C++ version of the PDB record I/O library above.
We have an open source implementation of a "virtual sphere" algorithm, which provides a means for interacting with an object in three-dimensions using a workstation mouse. This technique is similar to the one described in: M. Chen, S. Mountford, and A. Sellen, "A Study in Interactive 3-D Rotation Using 2-D Control Devices," Proceedings of SIGGRAPH '88, Computer Graphics 22, 4 (August 1988), pp.121-129.
Our Object Technology Framework (OTF) is an open source package for easily generating powerful C++ classes tailored to the needs and specifications of biochemical application developers.
Through our close relationship with the UCSF Nuclear Magnetic Resonance Laboratory, we develop and distribute applications for performing data analysis and display from magnetic resonance spectroscopy experiments. Available software includes MARDIGRAS, a package for calculating proton-proton distances from cross-peak intensities measured from a 2D NOE experiment, CORMA, a package for calculating the dipole-dipole relaxation matrix for a system of protons and converting that to intensities expected for a 2D NOE experiment, and SPARKY, an open source package for doing NOE cross peak assignments.
Autostereo is an open source package for developers to support adding multi-application stereo support on SGI IRIX workstations. The first application to use a stereo window will cause the video format to switch to stereo viewing and when the last application is done with stereo, the video format switches back. The package includes a small library for linking with applications and a daemon that can be invoked automatically by the library or placed in a X session file.
DMS is an open source program for computing the molecular surface of a molecule. It can distribute the computation across multiple hosts for maximal performance. The surface computed is that defined by F. M. Richards (1977, Ann. Rev. Biophys. Bioeng.). In addition to the molecular surface, DMS can report the molecular surface area associated with each atom, and surface normals at each surface point.
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