To install ProFit, unpack the tar file. This will create a ProFit directory with a src subdirectory.
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.
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.
Move the profit executable to somewhere in your path (e.g.
You should now create the environment variables
DATADIR. These should both point to the top ProFit directory where the
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
ProFit.help contains the help text displayed by the
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
ProFit V3.1 compiles under Windows using the open source
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:
Now change to the ProFit source directory:
Now run make by doing:
mingw32-make -f Makefile_dos
That will create the executable profit.exe
If you only wish to run ProFit from the DOS prompt command line, or
you are using Windows 95/98/ME, you can edit
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:
PATHvariable, such that the directory in which you have saved
profit.exeis added to your path (or move
profit.exeto 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.
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.