Some of the programs can make use of certain environment variables
(you can define values for them in your .cshrc file, for instance):
CCP4_OPEN is a CCP4 environment variable which determines
how new files are to be opened. All RAVE programs that may read CCP4
maps require that this variable is defined and set to UNKNOWN.
Recommended setting: setenv CCP4_OPEN UNKNOWN
OSYM is a variable which can be set to point to the
directory where the O-formatted spacegroup operator files are stored
(usually, this is $ODAT/symm/, where ODAT is another environment
variable which points to the local O data directory). Recommended
setting (Uppsala): setenv OSYM /home/gerard/lib/symm. Programs
which (sometimes) need symmetry operator files (most RAVE programs,
for instance) will use this if they can't locate an appropriate
symm-op file in your current directory.
GKPATH is a path that can be used to look for existing
(i.e., input) ASCII files in any program (except D-CUP), e.g. input
PDB files for MOLEMAN2 or LSQMAN, input mask files for MAMA, macro
files for MAPMAN, etc. Recommended setting (Uppsala): setenv
GKPATH '/nfs/pdb/full:./omac' (plus any directories from which
you often read files, e.g. ../cns or /home/me/models. GKPATH is a
list of directory names, separated by ":", which you frequently use
to read files from, but which you don't want to type in all the time.
Limitations: maximum length of GKPATH is 1,000 characters, and maximum
of 50 directories (each of max. 100 characters).
If you need to provide an existing ASCII file as input to any program
(except D-CUP), and you type a name that does not contain a directory
separator (i.e., a slash "/"), and the file does not exist in your
current directory, then the program will look in each of the directories
in GKPATH in turn to see if the file exists there. If it does, it
will be opened (and a message will be printed to remind you that the
file was found somewhere else than in your current directory). If the
file cannot be found in any directory, an error message will be given
Note: the mechanism to find O-style symmetry operator files using the
environment variable OSYM is a bit more involved and is not affected
by GKPATH. GKLIB on the other hand is superfluous, provided you
include your local library directory in GKPATH.
Note: to override the use of GKPATH, provide filenames with a prefixed
"./", e.g. in LSQMAN: read m1 ./1cel.pdb (this will only look for
the file "1cel.pdb" in the current directory).
GKLIB is a variable which can be set to point to a single
directory containing all library files. Several programs need their
own library file (e.g., DEJAVU, VOIDOO, MOLEMAN2, SOD, SEAMAN, MAPROP,
SPASM, RIGOR). When these programs ask you to supply the name of
their library file, the value of GKLIB (if defined) is prefixed
to the default library filename (saves typing long path names).
Recommended setting (Uppsala): setenv GKLIB /home/gerard/lib
GKBUFFER is a variable which defines the maximum
size of buffer arrays used for 2D plotting by O2D and LSQMAN.
The default is 500000 points (e.g., 500 by 1000). To override
the default, either set the environment variable GKBUFFER (e.g.,
setenv GKBUFFER 1000000), or provide it as a command-line
argument (e.g., run o2d gkbuffer 100000).
MAXHITS is a variable which defines the maximum
number of hits that will be generated by SPASM, RIGOR and DEJAVU.
This is done to prevent searches that would take years to
complete and that probably are due to unfortunate input-parameter
choices. This is particularly important for unsupervised use
of these programs, e.g. as part of web-based servers or
cron-driven scripts. The default value is set to 1000 and this
should be okay for most applications. To override the default,
either set the environment variable MAXHITS (e.g.,
setenv MAXHITS 100), or provide it as a command-line
argument (e.g., run spasm maxhits 5000).
MAPSIZE and MASKSIZE are environment variables which
work with several programs in the RAVE package. They can be used (with
the appropriate versions of these programs) to tell these programs how
much memory should be allocated for maps and masks, respectively. The
values of these environment variables can be over-ruled by specifying
command-line arguments (e.g.: run imp mapsize 10000000). Recommended
settings (Uppsala): setenv MAPSIZE 10000000 and
setenv MASKSIZE 5000000 (higher values for virus and
atomic-resolution work; lower values if you run the software on ESVs).
NUMMAPS is used by MAPMAN, and defines how many maps MAPMAN
can handle. Similarly, NUMMASKS defines the number of masks
that MAMA can have in memory at any one time. Recommended
settings (Uppsala): setenv NUMMAPS 2 and setenv NUMMASKS 4
(higher values for virus and atomic-resolution work; lower values if you
run the software on ESVs).
The maximum number of reflection data sets that DATAMAN can handle
is controlled by NUMSETS (max. 25), and the maximum number of
reflections per data set by SETSIZE. As with the other RAVE
programs, these parameters can be set as environment variables and/or
as command-line arguments. Recommended settings (Uppsala):
setenv NUMSETS 4 and setenv SETSIZE 200000 (higher values
for virus and atomic-resolution work).
The maximum number of sequences that SEQMAN can handle is controlled
by NUMSEQS, and the maximum sequence length by SEQLENG.
A number of programs now support start-up macros, i.e. macros that
are executed automatically when a program starts up. This is useful,
for instance, if you always work with X-PLOR files of nucleic acids
in LSQMAN (set the central atom to P and the chain-mode to XPlor).
or to set your standard grid and cell in MAMA (using the NEw commands).
The feature works by setting an environment variable to the name of
the file which contains your start-up macro. It is available in: