Starting the program

The program is started from the command line by typing the command:

   profit

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 HETATOMS command before reading in the structures (see Section 3.

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 COPT = in the Makefile is changed to COPT = -DGUNZIP_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 /tmp 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 also case insensitive; you may mix upper and lower case at will, though uppercase will be used throughout this documentation.

You exit from the program by typing QUIT.

Footnotes

... XMAS¹

XMAS is an XML-like file format developed at Inpharmatica, Ltd. which is designed for leaf-heavy data such as protein structure data