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Spock


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OS: Linux, Mac, ...





Spock is a full-featured molecular graphics program.

Features:

Display modes:

Spock can display and manipulate atoms, bonds, hydrogen bonds, solid and surfaces, CA traces, electrostatic potential contours, backbone worms, and even electron density maps. Spock can also calculate and display axis vectors for helices and sheets. Text labels and annotations are supported in a variety of fonts and colors.

Conferencing:

Spock allows real-time conferencing over the internet so that multiple sessions can be shared. Each spock session will display the same image and any participant can alter the display. The changes will be immediately communicated to all other participants in the conference. Best of all, this is accomplished in a low-bandwidth manner which doesn't require large graphics streams to be passed over the network which would give a slow response time. This leaves lots of bandwidth availible for desktop audio- or video-conferencing, allowing distant colleagues to collaborate and discuss structural data much more effectively.

Symmetry support:

Spock can display unit cells, and display all the symmetry replicates of a molecule within a given cell.

Modeling features:

Spock allows users to create and destroy bonds and hydrogen bonds, as well as rotate atoms around a bond. Atoms and residues may be independently repositioned, and residues can be mutated to other residues.

Viewpoint save and recall:

Users can save and recall up to 10 viewpoints in a structure for rapidly changing the view. Along with the orientation, information about what objects are displayed and what colors are currently assigned are saved.

Secondary structure editing:

Spock calculates secondary structure from atomic coordinates, or reads such information from PDB files and/or DSSP files. This information may be used to control the appearance of the backbone worm.

Image export:

The graphics view in spock can be exported to a variety of external rendering packages. Rather than just a bare-bones output file like those generated by most programs, the views exported by spock include almost the entire scene. For example, spock can serve as a graphical front end to MolScript, and is the easiest way to produce MolScript images around. For MolScript v 2.0, spock can even export molecular surfaces and electron density map contours for rendering by MolScript. Spock also exports views to VRML (both 1.0 and 2.0) for posting models on web pages, and Raster3D for photorealistic rendering. Spock can also generate movies of any session.

Data import:

Further, spock can read lots of external file types: DSSP structure assignment files, XPLOR density map files, MORASS interaction files, Grasp/DelPhi radius, charge, and size files, and phimap files. Finally, spock has an extensive interface to the energy minimization/molecular dynamics program AMBER, and can generate input files for amber with the push of a single button. Spock will also play back AMBER MD trajectory files, and can make movies. Since there are free converters for almost any structure file type to PDB-format, spock only directly handles that format.


Link: http://quorum.tamu.edu/


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