Helper applications

  The installer of spock should also see $SPOCK/bin/README, to determine if any of the supplied helper scripts need to be modified.

Spock interacts with a large number of external programs. Most of these programs are freely available from other sources, at least to academic users. If copies of these programs are not already in the default path, $SPOCK/bin is a good place to copy them. If they are not in the default path, or in this directory, spock will not be able to find them and thus will lose functionality.

The accessory programs spock may launch are:

• DSSP: this program may be launched from spock to determine the secondary structure of a protein. However, spock has it's own secondary structure calculation routines, so DSSP is not necessary. DSSP may be obtained from Chris Sander's group. See http://www.sander.embl-heidelberg.de/dssp/ for more information.  
• Molscript: spock can generate input files for Molscript (including version 2.0) and provides a convenient front-end to that program. Molscript may be obtained from http://www.avatar.se/molscript.  
• render: Spock can export images to Raster3D's render module. Raster3D may be obtained from: http://www.bmsc.washington.edu/raster3d/raster3d.html.  
• A PostScript previewer: Spock also uses a PostScript previewer such as xpsview or ghostview for previewing Molscript files. If one of these is not available, users will be unable to preview Molscript images. Ghostview is recommended and may be obtained from ftp://prep.ai.mit.edu/pub/gnu.    
• amber: spock can invoke amber to do energy minimization and molecular dynamics. Spock can read amber trajectory files for playback.  
• A WWW browser such as netscape or lynx: Spock uses an external WWW browser to display its on-line help.      

Spock can read some of the output of the following programs, but they are not launched from spock.

• Grasp/DelPhi: Spock can read radius and charge files in the format of these programs. Although spock calculates its own electrostatic potential fields, it can also read phimaps produced by these programs.  
• MORASS: spock can read the interactions file output by this program.  

Finally, these programs may be useful in conjunction with spock, but spock is not designed to directly interact with these programs

• mpeg_encode: This program can take a series of images (JPEG, most likely) such as produced by spock's movie mode and produce an MPEG-encoded movie from the images. The mpeg_encode package may be obtained from:

  ftp://mm-ftp.CS.Berkeley.EDU/pub/multimedia/mpeg/encode/      

• WhirlGif: This program can take a series of gif images and make a single animated gif for display on WWW pages. Again, spock's movie mode may be used to produce the series of images. WhirlGif may be obtained from:

  http://www.msg.net/utility/whirlgif/