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:
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.
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.
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
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.
