The environment for Bsoft requires the following variables for correct functioning:
BSOFT: Points to the root of the Bsoft tree used to define other variables and for external packages requiring the Bsoft library.
BSOFT32: Points to the 32-bit version of Bsoft on systems supporting separate 32- and 64-bit libraries (IRIX and Linux).
PATH: Allows the binaries to be found.
LD_LIBRARY_PATH: Allows the Bsoft library to be found.
BPARAM: Points to a directory with parameter files for information such as atomic masses, structure factors, symmetry parameters and residue properties needed for several programs.
During compilation, the bmake script generates two files, bsoft.cshrc and bsoft.bashrc, which contain default environmental parameters for Bsoft. These files can be sourced to set up the paths to the Bsoft executables and libraries.
The Unix csh syntax to set the required environmental variables is:
setenv BSOFT /usr/local/bsoft
setenv PATH ${BSOFT}/bin:$PATH
setenv LD_LIBRARY_PATH ${BSOFT}/lib:$LD_LIBRARY_PATH
setenv BPARAM ${BSOFT}/parameters
Alternatively, users of the bash shell should set it as follows:
BSOFT=/usr/local/bsoft
export BSOFT
PATH=${BSOFT}/bin:$PATH
export PATH
LD_LIBRARY_PATH=${BSOFT}/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH
BPARAM=${BSOFT}/parameters
export BPARAM
The LD_LIBRARY_PATH might have different forms on different platforms. On IRIX64, the LD_LIBRARYN32_PATH and LD_LIBRARY64_PATH distinguish between the 32-bit and 64-bit versions of the library. On Mac OSX, DYLD_LIBRARY_PATH is used.
The environmental variables for command line access is the same as for other Unix platforms, except that the variable pointing to the libraries is:
DYLD_LIBRARY_PATH
Applications designed to be launched from the Dock or Finder in Mac OSX use a hidden directory, ".MacOSX" with a property list file "environment.plist" specifying the environmental parameters. The "macinstall" script in the macosx directory will install the Tcl/Tk programs "bshow" and "brun", and set up the environment in the current account logged in. To have the Finder read the .MacOSX/environment.plist file, the user needs to log out and log back in.
Paths to the executables must be set (typically in the LOGIN.COM script) as follows:
A symbol for each program:
BIMG == "$ $DISK:[BSOFT.BIN]BIMG.EXE"
OR a path to all programs
DEFINE DCL$PATH $DISK:[BSOFT.BIN]
Parameters such as atomic masses, structure factors, symmetry parameters and residue properties are needed for several programs, and the following environmental variable must be set:
BPARAM == "[BSOFT.PARAMETERS]"