Introduction

Spock is a high-end molecular graphics package for displaying protein and nucleic acid structures. Spock also is a powerful search engine allowing users to search through a directory of PDB files for proteins which have specific characteristics. Spock provides the typical molecular visualization views (ribbons of several types, line and rod bonds, etc.) as well as molecular and accessible surfacing routines. Spock also provides interfaces to DSSP for reading in secondary structure information and a near-WYSIWYG (what you see is what you get) interface for Molscript for producing publication-quality printouts. Of course, the graphics images in spock can be saved in several formats for presentation graphics as well.

Major features:

• Based on OpenGL for maximum portability, with an easy to use, intuitive, graphical user interface.

• Available for IRIX (SGI), SunOS (Sun), and Linux for PC's.

• Dynamic memory allocation so there are no hard-coded upper limits on the size of structures, or the resolution of surfaces. We've had over 140,000 atoms loaded with no problems, and have constructed surfaces on a 128x128x128 grid.

• Variety of bond display modes including line, ball-and-stick, and cylinder styles.

• Backbone ribbons are also available in a variety of styles, including tubular, rectangular, secondary structure, and a variable radius style, where the radius of the ribbon is proportional to some property such as B-factor, or genetic diversity.

• Calculate and display molecular and accessible surfaces.

• Calculate and display 2D and 3D isopotential contours.

• Determines Hydrogen bonding patterns from structure; Determines secondary structure from this data. Can also read a DSSP file to determine secondary structure.

• Ability to save and easily switch between multiple views of a structure.

• Ability to define and independently manipulate subsets of atoms. Subsets may overlap, and can by dynamically re-defined.

• SGI version supports hardware stereo (Crystal Eyes). All versions have side-by-side stereo.

• Simple modeling features: dynamic bond editing, rotation of torsion angles, simple mutation facility.

• Powerful history and macro mechanism for creating shortcuts to complex scripts. There's also a text-only mode for remote sessions and for off-line processing of scripts.

• Command line accepts and translates environment variables. Can also set environment variables from the command line for spock and any subprocesses. This allows for user customization of commands and definition of shortcuts.

• Calculate and display axis of helices, and major moment of sheets.

• Exports model to: Molscript, Raster3D, VRML v1.0, and VRML v2.0. This provides a what-you-see-is-what-you-get (WYSIWYG) interactive interface to these formats.

• Powerful built-in function calculator makes it easy to apply functions to atomic or surface properties, with user-definable functions and variables.

• Supported image formats: RGB/Iris, Sun Raster file image, GIF, TIFF, PPM, FBM, and PostScript. JPEG is no longer supported since it lead to version-skew problems on many platforms, and JPEG isn't a good format for the type of images spock produces anyway.

• Powerful selection mechanism to easily specify groups of atoms or molecules.

• Integrated help facility using an external WWW browser, with context-sensitive help. Help on each menu item is also optionally displayed on the status line for novice users.