Installation

To install ProFit, unpack the tar file. This will create a ProFit directory with a src subdirectory.

Compiling under UNIX-like operating systems

After unpacking the tar file, go into the src subdirectory of the ProFit directory. It is possible to edit the Makefile to allow the (optional) support for the XMAS library, the GNU Readline library or decompression of gzipped PDB files.

Type:

      make

to create an executable file called `profit'.

Under recent Linux installations, GNU Readline support should just work. Uncomment the two lines in the Makefile:

      READLINE    = -DREADLINE_SUPPORT
      READLINELIB = -lreadline -lcurses

and compile as normal. You may need to install the readline development libraries first, which is done with a command like:

      yum install readline-devel         (RPM-based systems)
      apt-get install libreadline5-dev   (Debian-based systems)

On other systems, you will need to obtain and install readline. See: http://directory.fsf.org/project/readline/

If you need to install GNU readline manually, some notes are supplied in Section 17.

Installing under UNIX-like operating systems

Move the profit executable to somewhere in your path (e.g. ~/bin/ or /usr/local/bin)

You should now create the environment variables HELPDIR and DATADIR. These should both point to the top ProFit directory where the files ProFit.help and mdm78.mat are stored. e.g.

(csh)   setenv HELPDIR /home/andrew/ProFitV3.1
        setenv DATADIR /home/andrew/ProFitV3.1
(sh)    export HELPDIR=/home/andrew/ProFitV3.1
        export DATADIR=/home/andrew/ProFitV3.1

mdm78.mat is the Dayhoff amino acid similarity scoring matrix while ProFit.help contains the help text displayed by the help command.

Alternatively, you may wish to store these files elsewhere, or have all help files and data files in a single directory.

Under VAX/VMS-like operating systems, these should be ASSIGNs. e.g.

      ASSIGN $A:[ANDREW.PROFIT] DATADIR
      ASSIGN $A:[ANDREW.PROFIT] HELPDIR

Compiling under DOS/Windows operating systems

ProFit V3.1 compiles under Windows using the open source mingw compiler. See the mingw web site for details: http://www.mingw.org/wiki/HOWTO_Install_the_MinGW_GCC_Compiler_SuiteIt should also compile cleanly using commercial compilers such as the Microsoft, Intel or Borland compilers (though this has not been tested).

To compile with mingw, first open a DOS shell and ensure that the mingw binary directory from your installation of mingw is in your path. For example:

      PATH=%PATH%;C:\Qt\2009.01\mingw\bin

Now change to the ProFit source directory:

      cd ProFitVx.y\src

Now run make by doing:

      mingw32-make -f Makefile_dos

That will create the executable profit.exe

Installing under DOS/Windows operating systems

If you only wish to run ProFit from the DOS prompt command line, or you are using Windows 95/98/ME, you can edit C:\autoexec.bat and add the lines

      PATH=%PATH%;C:\My Documents\ProFitV3.1\src
      SET HELPDIR=C:\My Documents\ProFitV3.1
      SET DATADIR=C:\My Documents\ProFitV3.1

(Note no double-inverted commas or escaping is required for spaces in directory names.)

This will put the profit executable in your path and set the two environment variables. Of course you can move the files anywhere you want and modify the above commands as required.

If you are using Windows NT/2000/XP or later, you must set environment variables as follows:

1. Open Control Panel
2. Click the System icon
3. Go to the Advanced pane
4. Click the Environment Variables button
5. Select the new button to create a new environment variable
6. Enter the variable name and value in the appropriate boxes, creating HELPDIR and DATADIR as above.
7. Edit the PATH variable, such that the directory in which you have saved profit.exe is added to your path (or move profit.exe to a directory already in your path).

Alternatively, if you only plan to run ProFit by double-clicking its icon, simply ensure that

      profit.exe
      mdm78.mat
      ProFit.help

are all in the same directory. Double clicking the ProFit icon will then find the required files automatically.

The Rotation Bug

There is a known (but rarely seen) bug with ProFit where a fitted structure may be fitted 180 degrees away from its optimum fit. This only seems to affect fitting of identical structures and appears to result from a saddle point in the RMS surface resulting in apparent convergence. While the effort to correct the bug is ongoing we have taken steps to fix the effect of the bug.

Compiling with GCC with optimization on (-O3) seems to hide the bug. Alternatively, editing the Makefile and uncommenting the line

      ROTATEREFIT = -DROTATE_REFIT

will result in ProFit rotating a fitted structure (42 degrees, Z axis), refitting the structure then selecting the better fit.