Customization

  Spock reads the from a system-wide file $SPOCK/Spockrc to obtain customizable parameters, and some setup information. This file is in the format of a spock history/command file (§7), but it should be obvious how to edit the supplied version to suit local needs. The majority of the file is concerned with setting environment variables to be used by spock and its sub-processes. Users can override the system-wide configuration with their own .spockrc file, which is read from the user's home directory. (In fact, users can create several .spockrc files, one for each project, if they wish, as this proves to be a convenient way to set up spock for a particular structure). The environment variables used are discussed below:

Paths:

These variables set up the default paths that spock uses for many of its operations.

• SP_AALIB: The default directory for the the amino acid library used for several commands including sorting, mutation, and hydrogen bonding. If you wish to modify these files, it would be best to make a personal aalib directory and copy the contents of the system directory into it.
• SP_SYMMETRY_LIB: The default location of the symmetry library.
• SP_DSSP: Sets the default location of DSSP files.
• SP_HISTORY: Sets the default location of spock history/command files.
• SP_IMAGE: Sets the default location of image output files. These files include graphics images as well as Molscript files, Raster3D files, and VRML files.
• SP_HELP_PATH: The path to the help files (usually $SPOCK/doc/). However, the if for some reason there's no local copy of the manual, you may use the URL:

  http://quorum.tamu.edu/jon/spock.

• SP_PDB: Sets the default location of PDB files.
• SP_XPLOR: Sets the default location of XPLOR files.

License information:

• SP_DOMAIN: Spock's license verification routines need to know the local domain. Set this to the local domain, but do not use a leading period. For example here at Texas A&M, we use set $SP_DOMAIN=tamu.edu.

External commands/Help:

  The on-line help system, previewing and printing commands use these variables. For on-line help, spock uses an external WWW browser.  

• SP_BROWSER: The WWW browser to use for help files (e.g. netscape, lynx)
• SP_HELP: The path to the help command (usually $SPOCK/bin/sphelp).
• SP_PRINT_CMD: The command used to print (e.g. lp, xprint). This command must read be able to serve as the tail end of a unix pipe (i.e. it must read the file from standard input.)
• SP_IMGVIEW: The prefered image previewer to use. By default this is SGI's imgview, although you can change it to any image previewer. This is used primarily for the Raster3D previewing option.

Other variables set by spock:

Model information:

The following variables are not set by the installation scripts, but are instead set each time spock reads a PDB file, or creates or destroys a vertex subset. They are intended to be useful for command scripts, etc., and are listed here for completeness.

• SP_ATOMCNT: the number of currently loaded atoms
• SP_MOLCNT: the number of currently loaded molecules
• SP_MDLCNT: the number of currently loaded models
• SP_RESICNT: the number of currently loaded residues
• SP_RESOLUTION: the resolution of the last pdb file read
• SP_NVSUBS: the number of vertex subsets defined
• SP_NSUBS: the number of atom subsets defined

Statistics:

The following variables are set when the user performs a statistics calculation via the ``Calculate properties'' menu (§6.6.2). They are intended to be used by command scripts §7 or the command-line calculator § 5.5.  

• SP_N, the number of items in the property
• SP_MEAN, the mean
• SP_MEDIAN, the median
• SP_SD, the standard deviation
• SP_MAX, the maximum value
• SP_MIN, the minimum value
• SP_Q1, the first quartile
• SP_Q3, the third quartile
• SP_IQR, the inter-quartile range
• SP_SUM, the sum of the data values.