If you have the CCP4 suite of programs up-and-running on your machine and if the space group of your crystals is not centrosymmetric, all you need is a .mtz file containing your data. Then give something like : graphent mydata.mtz (to use all data), or, graphent 15 3.5 mydata.mtz (to define resolution limits), or, graphent h0l 15 3.5 mydata.mtz (to use only the h0l terms), and you will be presented with a smallish window from which you can choose the columns you wish to use for your intended synthesis. If the symbol graphent is not defined, please read the installation section of this manual (6.1).
Now, the difficult bit. The order with which you click on the columns to select them is important : you must select first the amplitude terms (with their standard deviation), followed (possibly) by phase angles, and finally figure-of-merit. If you choose columns with the wrong order the program will not cooparate. To see what column type combinations (and in what order) are supported by the program click on "HELP" in the dialog window.
Please note that not all conceivable types of syntheses are supported by the program. If your intended synthesis is not listed in the "HELP" screen of the dialog, you will have to use sftools to reduce the synthesis you have in mind to a recognisable (by GraphEnt) combination.
If all goes well, the dialog window will disapper (possibly after asking you
to confirm a setting by just pressing 'y' or 'n'), and then you should see
a section from the conventional map, followed (after some time) by a window
showing the same section from the GraphEnt map. That second window will be
updated as the calculation progresses, until convergence is achieved.
When the calculation is over, a third window will appear containing a graph
of the contributions of the various reflections to the 
test.
If you
are calculating a difference Patterson synthesis, the first window you will
see is the normal probability plot for your data.
Hit <RETURN> in the unix shell (where you started the calculation from) to exit the program. The directory should contain (in-between other files) the basic output from the program, namely the GraphEnt map : maxent.map.