The program is started from the command line by typing the command:
Once the program is started, you may read in structures to be fitted. Alternatively, the PDB files may be specified on the command line:
profit reference.pdb mobile.pdb
By default, ProFit does not read HETATM records from the PDB file. This may be changed from the command line by using the -h flag:
profit -h profit -h reference.pdb mobile.pdb
Alternatively, once in the program you may give the
command before reading in the structures (see Section 5).
ProFit can run a script file, a text file of ProFit commands, from the command line using the -f flag:
profit -f myscriptfile.txt profit -f myscriptfile.txt -h reference.pdb mobile.pdb
Once in the program you may use the command
to run a script file (see Section 14).
If compiled with XMAS1 file support, the
-x flag may
be used to specify that the files named on the command line are XMAS
files instead of PDB files. Note that the program currently will only
write PDB format files.
profit -x reference.xmas mobile.xmas
If compiled with GUNZIP support
then the program can read gzipped PDB files. This will only work on
unix-like platforms and assumes that the
gunzip program is in
your path. Note that the uncompressed files will remain in
with a name like
readpdb_12345 where 12345 is a process
number. You will need to delete these regularly!
Once in the program, you issue commands by typing at the keyboard. These commands may always be abbreviated to the minimum non-ambiguous string. The program is mostly case insensitive; you may mix upper and lower case at will, though uppercase will be used throughout this documentation. The only times that ProFit will be case sensitive are when dealing with file names or lowercase chain identifiers (see Section 9).
Support for the GNU Readline library2 was introduced in ProFit V3.0 allowing you to edit the command line and to recall previous commands. Again, this is a compile time option.
You exit from the program by typing