File names in the scanps_defaults.dat file MUST NOT be fully qualified. Thus,
MATRIX_FILE nmd.mat
will look in the users' current directory for the file. If the matrix file was in /data/local/scanps/matrices you would have to define:
MATRIX_DIR /data/local/scanps/matrices/
as well.
This is also true of the binary database files. The directory for these may be defined by DB_DIR. e.g.
DB_DIR /data/local/databases/scanps/ BDB_ROOT pir66
would look for the files pir66.bix and pir66.bsq in the directory /data/local/databases/scanps.
The only other directory that can be specified in this way is GENERAL_DIR, this holds "other" files needed by the program. At the moment, the only file that is put in GENERAL_DIR is the CODON_FILE for use with DNA vs protein comparisons. More of that later...