Available CGL Software

Full source code for all of our software distributions is available. Licensing terms vary with the package. The available packages are:
Actively developed and maintained software

ChimeraX

extensible molecular visualization and analysis application -- successor to UCSF Chimera

Cytoscape plugins

visualization plugins such as StructureViz and ChemViz

Available but unsupported software

UCSF Chimera

extensible molecular visualization and analysis application

TOPO2

create transmembrane proteins images

MinRMS

tool for determining protein similarity

PDB record I/O libraries

read/write PDB files

KSDSSP

compute protein secondary structure

Virtual sphere

3D manipulation with a mouse

SPARKY

NMR spectrum assignment

Stereotest

Simple OpenGL Stereo Test Program

Deprecated software

MidasPlus

molecular visualization

DMS

compute molecular surfaces

SGI OpenGL stereo software

automatically switch SGI stereo mode

TOPO2

The TOPO2 program is an open source program written in Python for the creation of transmembrane protein 2D topology images. It makes no attempt to predict the TMDs that it displays. The user needs to supply that information. Residues of interest can be highlighted, if desired.

PDB Record I/O Libraries

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

The ksdssp program 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.

Virtual Sphere

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.

SPARKY: NMR Spectrum Analysis Software

Through our close relationship with the UCSF Nuclear Magnetic Resonance Laboratory, we developed SPARKY, an open source package for doing NOE cross peak assignments. Development and maintenance has now been taken over by the NMR Facility at Madison and renamed NMRFAM-SPARKY.

Stereotest

The stereotest program is a simple OpenGL program for troubleshooting OpenGL 3D stereo in a window on Linux and Windows. Binaries and source are available.

Deprecated Software

MidasPlus

UCSF ChimeraX is extensible molecular modeling system that has supplanted Midasplus and Chimera. We are no longer distributing this software.

The MidasPlus application (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.

DMS

NOTE: If you are using DMS to generate UCSF DOCK input, it is much easier to use UCSF Chimera's Write DMS tool instead.

The DMS program is an open source program written in C 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 surface point, and surface normals at each surface point.

DMS may be downloaded either in zip or shar format. The zip archive (dms.zip) can be expanded using either the "unzip" command or any zip utility program. The shar archive (dms.shar) can be extracted with the command sh < dms.shar from a Unix or Cygwin shell. In either case, the result should be a "dms" directory that contains the source to DMS as well as a README file describing how to compile DMS.

SGI OpenGL Stereo Software

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.